[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $sbst_model = 'HKY85' will be changed to 'TN93' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $resfreq = 'e' will be changed to '0.25,0.25,0.25,0.25' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $gaprate = '0.025' will be changed to 'Dawgx0.71251' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $gapext = '0.75' will be changed to '0.3957' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $if_insopen_forever = '0' will be changed to '1' ...


<<<<<<< Program name: classify_msa_errors_via_mblks.2val.pl (path: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/Scripts/classify_msa_errors_via_mblks.2val.pl) >>>>>>>>

Current working directory: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/class_0001/lclid_0000002 .

Binary programs:
     (for tree inference)  /Users/kezawa3/Bioinformatics/PhyML/Compiled/bin/phyml ,
Source control file (for PhyML): Not used .
Source file of substitution model (for PhyML): Not used .

Sequence type: Nucleotide .

Input files:
     (Tree)      /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/dawg_inp0000002.txt .

    (anchor MSA) /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/refaln.0000002.aln .

   (simulation parameters} /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/dawg_inp0000002.txt,
   (reference MSA)         /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/refaln.0000002.aln,
   (reconstructed MSA)     /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/recaln.0000002.aln,
   (list of segments)      /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/equiv_rgs_brief.0000002.txt .

Directory for interim output files for tree inference: Interim/Infer_tree .

Interim output list of candidate trees:  {topoutdir}/tree_whole_full.txt .
Temporary directories for PAML (obsolete):  {top_tmpdir}/s{seg_id}/g{indx_gpattern}/t{indx_tree}/,
   where {top_tmpdir} = Interim/Tmp/Ref for the reference MSA,
                      = Interim/Tmp/Rec for the reconstructed MSA.

Summary outputs:
   (1st Round) tbl_summ_class_msa_errors.1.txt ,
   (2nd Round) tbl_summ_class_msa_errors.2.txt .

Directory for the log files: {log_dir} = LogFiles .

Log files:
   (for candidate tree enumeration) {log_dir}/log_tree_whole_full.txt .

   (for analyzing the reference & reconstructed MSAs for each segment) {log_dir}log_seg_anal.{seg_id}.txt .

* All the temporary outputs will be removed .

Parameters for tree inference (via PhyML):

   Substitution model:  TN93 .
   (Model for PhyML: HKY85 .)

   #{Substitution rate categories}: 1 .
   Gamma shape parameter for the rate variation across sites: 0 .
   Tree topology search method: NNI .
   Option on what to do with the residue frequencies: 0.25,0.25,0.25,0.25 .


   Transition/transversion ratios:
        (for A <-> G) 1 ,
        (for T <-> C) 1 ,
       (average (to be used for PhyML (if applicable))) 1 .



Options for PhyML shared by both tree inference and column-wise likelihood calculation:

   $OPTIONS_SHARED = ' -d nt -c 1 ' .


Levels of tests for debugging or behavior tests:

   $TEST_LEVEL_VAL    =  1 ,

   $TEST_LEVEL        =  0 ,
   $TEST_LEVEL2       =  0 ,
   $TEST_LEVEL_newtype   = 0 ,
   $TEST_LEVEL_cipc   = 0 ,
   $TEST_LEVEL_cipc2   = 0 ,
   $TEST_LEVEL_umlp   = 0 ,
   $DBG_LEVEL_EXPHYML =  0 ,
   $FLG_RMV_TMPOUT    =  1 .


Parameters in the Perl package 'MyMalnComparison.pm':

$MyMalnComparison::TEST_LEVEL_lc  = 0 .


Parameters in the Perl package 'MyTreeMap_indels_spt_odr.pm':

$MyTreeMap_indels_spt_odr::UPPER_BOUND_ANAL_LEN_GBCLS = 150 ,
$MyTreeMap_indels_spt_odr::UPPER_BOUND_ANAL_GAPLEN = 120 .



<<<<< Now, read in the list of segments >>>>>


#{segments} = 48

Seg_ID	Start_in_Ref	End_in_ref	Start_in_Rec	End_in_Rec	Diagnosis

0	0	0	0	0	IDENTICAL
1	7	30	7	24	CLEARLY_DIFFERENT
2	35	42	29	35	CLEARLY_DIFFERENT
3	45	56	38	49	CLEARLY_DIFFERENT
4	57	178	50	171	CLEARLY_DIFFERENT
5	192	296	185	288	CLEARLY_DIFFERENT
6	304	317	296	309	CLEARLY_DIFFERENT
7	326	336	318	328	CLEARLY_DIFFERENT
8	349	389	341	381	CLEARLY_DIFFERENT
9	395	398	387	390	CLEARLY_DIFFERENT
10	404	467	396	451	CLEARLY_DIFFERENT
11	474	476	458	460	CLEARLY_DIFFERENT
12	483	489	467	473	CLEARLY_DIFFERENT
13	517	523	501	507	CLEARLY_DIFFERENT
14	538	546	522	530	CLEARLY_DIFFERENT
15	549	553	533	537	CLEARLY_DIFFERENT
16	557	606	541	589	CLEARLY_DIFFERENT
17	619	622	602	605	CLEARLY_DIFFERENT
18	629	654	612	636	CLEARLY_DIFFERENT
19	676	691	658	671	CLEARLY_DIFFERENT
20	772	809	752	788	CLEARLY_DIFFERENT
21	825	829	804	807	CLEARLY_DIFFERENT
22	837	854	815	830	CLEARLY_DIFFERENT
23	866	880	842	856	CLEARLY_DIFFERENT
24	885	887	861	863	CLEARLY_DIFFERENT
25	890	953	866	929	CLEARLY_DIFFERENT
26	957	960	933	936	CLEARLY_DIFFERENT
27	976	979	952	955	CLEARLY_DIFFERENT
28	984	986	960	962	CLEARLY_DIFFERENT
29	991	995	967	971	CLEARLY_DIFFERENT
30	1001	1010	977	986	CLEARLY_DIFFERENT
31	1012	1016	988	992	CLEARLY_DIFFERENT
32	1060	1085	1036	1056	CLEARLY_DIFFERENT
33	1093	1096	1064	1067	CLEARLY_DIFFERENT
34	1104	1161	1075	1132	CLEARLY_DIFFERENT
35	1162	1213	1133	1184	CLEARLY_DIFFERENT
36	1214	1216	1185	1187	CLEARLY_DIFFERENT
37	1217	1219	1188	1190	CLEARLY_DIFFERENT
38	1231	1272	1202	1236	CLEARLY_DIFFERENT
39	1279	1283	1243	1247	CLEARLY_DIFFERENT
40	1304	1340	1268	1304	CLEARLY_DIFFERENT
41	1354	1356	1318	1320	CLEARLY_DIFFERENT
42	1363	1365	1327	1328	CLEARLY_DIFFERENT
43	1403	1414	1366	1374	CLEARLY_DIFFERENT
44	1457	1464	1417	1422	CLEARLY_DIFFERENT
45	1467	1530	1425	1476	CLEARLY_DIFFERENT
46	1536	1539	1482	1485	CLEARLY_DIFFERENT
47	1553	1555	1499	1501	IDENTICAL



<<<<< Now, read in the reference MSA >>>>>

#{sequences in MSA} =  15 .
#{columns in MSA}   = 1555 .


<<<<< Now, read in the reconstructed MSA >>>>>

#{columns in MSA} = 1501 .


<<<<< Now, read in the core alignment (to be fed into tree reconstruction, if necessary) >>>>>

#{columns in MSA} = 1555 .


<<<<< Now, give nominal frequencies to the residues >>>>>



<< Residue frequencies estimated from the core alignment >>

Residue	Frequency

A	0.2500000
C	0.2500000
G	0.2500000
T	0.2500000



<<<<< Reading-in the Input Tree >>>>>


<<<<< Now, create an interim file recording the input trees >>>>>


<<<<< Now, calculate the Akaike weights of the candidate trees and necessary inputs  >>>>>


<<<<< Now, Output candidate trees, their Akaike weights, and their attributes  >>>>>

< The 0 th candidate tree (topnode ID: 29; Log_Akaike_weight = 0) >

Sum (-log(Pv)) = NA
log (Prob(MSA|Tree)_ML) = NA
#{free parameters} = NA
AIC = 0
BIC = 0

( seq0020{28}:0.1529, ( seq0018{26}:0.1741, ( ( seq0015{23}:0.1492, ( seq0013{20}:0.1827, seq0014{21}:0.1659 ){22}:0.0049 ){24}:0.0297, ( ( seq0008{16}:0.0865, seq0009{17}:0.1286 ){18}:0.0335, ( ( seq0005{10}:0.0368, ( seq0006{11}:0.0286, seq0007{12}:0.0362 ){13}:0.0065 ){14}:0.0368, ( ( seq0000{1}:0.0054, seq0001{2}:0.0081 ){3}:0.0232, ( seq0002{4}:0.0189, ( seq0003{5}:0.0124, seq0004{6}:0.0108 ){7}:0.0070 ){8}:0.0270 ){9}:0.0205 ){15}:0.0703 ){19}:0.0383 ){25}:0.0314 ){27}:0.0130 ){29};

Branch_ID	length	P-value	parent_node_ID

1	0.0054	NA	3
2	0.0081	NA	3
3	0.0232	NA	9
4	0.0189	NA	8
5	0.0124	NA	7
6	0.0108	NA	7
7	0.0070	NA	8
8	0.0270	NA	9
9	0.0205	NA	15
10	0.0368	NA	14
11	0.0286	NA	13
12	0.0362	NA	13
13	0.0065	NA	14
14	0.0368	NA	15
15	0.0703	NA	19
16	0.0865	NA	18
17	0.1286	NA	18
18	0.0335	NA	19
19	0.0383	NA	25
20	0.1827	NA	22
21	0.1659	NA	22
22	0.0049	NA	24
23	0.1492	NA	24
24	0.0297	NA	25
25	0.0314	NA	27
26	0.1741	NA	27
27	0.0130	NA	29
28	0.1529	NA	29



 ... Confirmed that all interior nodes of this tree have 2 child nodes each ...


 ... The subroutine 'make_node2abs_depth' Ended ...


 ... The subroutine 'make_node2ct_exoffs' Ended ...

Node_ID	Depth	#{exteior_offsprings}

1	8	1
2	8	1
3	7	2
4	8	1
5	9	1
6	9	1
7	8	2
8	7	3
9	6	5
10	7	1
11	8	1
12	8	1
13	7	2
14	6	3
15	5	8
16	6	1
17	6	1
18	5	2
19	4	10
20	6	1
21	6	1
22	5	2
23	5	1
24	4	3
25	3	13
26	3	1
27	2	14
28	2	1
29	1	15



Seq_indx	Seqname	Node_ID

0	seq0000	1
1	seq0001	2
2	seq0002	4
3	seq0003	5
4	seq0004	6
5	seq0005	10
6	seq0006	11
7	seq0007	12
8	seq0008	16
9	seq0009	17
10	seq0013	20
11	seq0014	21
12	seq0015	23
13	seq0018	26
14	seq0020	28






<<<<<<< The Main Analyses: Classify the MSA Errors in each Erroneous Segments by comparing Reference & Reconstructed segmental MSAs. >>>>>>>

<<<<<< Segment ID: 1  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (23, 17)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 1 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 23 ,
#{columns in new reconstructed MSA} = 17 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22

seq0000   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -
seq0014   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    0    0    0    -    -    -    -    -    -
seq0015   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0006   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0007   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0008   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0015   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	2	1	0	0	0	0
2nd(reconstructed)	1	1	0	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Merge(complementary)	2	21:0:2:X/21:8:13:-	21:8:10:-
2nd(reconstructed)	Complex(???)	100	15:17:22:-	15:11:13:-/18:14:16:X


{Total penalty} = 102 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 17 ,
#{columns in new reconstructed MSA} = 17 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0006   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0007   	    0    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0008   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0014   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0   -6   -6   -6    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -
seq0014   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	0	1	0	3
2nd(reconstructed)	1	0	0	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	11	21:8:13:-/15:17:22:-	25:11:16:-/23:11:16:X/20:11:16:X/18:11:16:X
2nd(reconstructed)	Complex(???)	100	21:0:2:X	20:14:16:X


{Total penalty} = 111 .





 --- Finished analysis for the segment 1 ! ---

<<<<<< Segment ID: 2  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (7, 6)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 2 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 2 ! ---

<<<<<< Segment ID: 3  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (11, 11)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 3 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 11 ,
#{columns in new reconstructed MSA} = 11 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    -    1    0    0    0    0    0    0    -    -    -
seq0001   	    -    1    0    0    0    0    0    0    -    -    -
seq0002   	    -    1    0    0    0    0    0    0    -    -    -
seq0003   	    -    1    0    0    0    0    0    0    -    -    -
seq0004   	    -    1    0    0    0    0    0    0    -    -    -
seq0005   	    -    1    0    0    0    0    0    0    -    -    -
seq0006   	    -    1    0    0    0    0    0    0    -    -    -
seq0007   	    -    1    0    0    0    0    0    0    -    -    -
seq0008   	    -    1    0    0    0    0    0    0    -    -    -
seq0009   	    -    1    0    0    0    0    0    0    -    -    -
seq0013   	    -    1    0    0    0    0    0    0    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    1    0    0    0    0    0    0    -    -    -
seq0018   	    -    1    0    0    0    0    0    0    -    -    -
seq0020   	    -    1    0    0    0    0    0    0    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    -    -    -    -    3    3    3    3    3    3    3
seq0001   	    -    -    -    -    3    3    3    3    3    3    3
seq0002   	    -    -    -    -    3    3    3    3    3    3    3
seq0003   	    -    -    -    -    3    3    3    3    3    3    3
seq0004   	    -    -    -    -    3    3    3    3    3    3    3
seq0005   	    -    -    -    -    3    3    3    3    3    3    3
seq0006   	    -    -    -    -    3    3    3    3    3    3    3
seq0007   	    -    -    -    -    3    3    3    3    3    3    3
seq0008   	    -    -    -    -    3    3    3    3    3    3    3
seq0009   	    -    -    -    -    3    3    3    3    3    3    3
seq0013   	    -    -    -    -    3    3    3    3    3    3    3
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    3    3    3    3    3    3    3
seq0018   	    -    -    -    -    3    3    3    3    3    3    3
seq0020   	    -    -    -    -    3    3    3    3    3    3    3





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	21:1:1:-	21:0:0:-
2nd(reconstructed)	Merge(same-type)	2	21:0:0:-/21:8:10:-	21:0:3:-


{Total penalty} = 3 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 11 ,
#{columns in new reconstructed MSA} = 11 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    0    -    -    -    -    3    3    3    3    3    3
seq0001   	    0    -    -    -    -    3    3    3    3    3    3
seq0002   	    0    -    -    -    -    3    3    3    3    3    3
seq0003   	    0    -    -    -    -    3    3    3    3    3    3
seq0004   	    0    -    -    -    -    3    3    3    3    3    3
seq0005   	    0    -    -    -    -    3    3    3    3    3    3
seq0006   	    0    -    -    -    -    3    3    3    3    3    3
seq0007   	    0    -    -    -    -    3    3    3    3    3    3
seq0008   	    0    -    -    -    -    3    3    3    3    3    3
seq0009   	    0    -    -    -    -    3    3    3    3    3    3
seq0013   	    0    -    -    -    -    3    3    3    3    3    3
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    -    -    -    -    3    3    3    3    3    3
seq0018   	    0    -    -    -    -    3    3    3    3    3    3
seq0020   	    0    -    -    -    -    3    3    3    3    3    3



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    -    -    -    -    4    0    0    0    0    0    0
seq0001   	    -    -    -    -    4    0    0    0    0    0    0
seq0002   	    -    -    -    -    4    0    0    0    0    0    0
seq0003   	    -    -    -    -    4    0    0    0    0    0    0
seq0004   	    -    -    -    -    4    0    0    0    0    0    0
seq0005   	    -    -    -    -    4    0    0    0    0    0    0
seq0006   	    -    -    -    -    4    0    0    0    0    0    0
seq0007   	    -    -    -    -    4    0    0    0    0    0    0
seq0008   	    -    -    -    -    4    0    0    0    0    0    0
seq0009   	    -    -    -    -    4    0    0    0    0    0    0
seq0013   	    -    -    -    -    4    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    4    0    0    0    0    0    0
seq0018   	    -    -    -    -    4    0    0    0    0    0    0
seq0020   	    -    -    -    -    4    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	2	1	0	0	0	0
2nd(reconstructed)	1	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Merge(same-type)	2	21:1:1:-/21:8:10:-	21:1:4:-
2nd(reconstructed)	Shift	1	21:1:4:-	21:0:3:-


{Total penalty} = 3 .





 --- Finished analysis for the segment 3 ! ---

<<<<<< Segment ID: 4  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (121, 121)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

[WARNING 'cal_init_psm_cands_for_twin_msas'] Found 3 gaps longer than 120. So, I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 4 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


<<<<<< Segment ID: 5  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (104, 103)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 11) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 5 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 4) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 4 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 103 ,
#{columns in new reconstructed MSA} = 103 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	  -68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    -    3    3
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3    -    -    -    -    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    3   -1   -1
seq0009   	    3   -1   -1
seq0013   	   -1   -1   -1
seq0014   	   -1   -1   -1
seq0015   	   -1   -1   -1
seq0018   	   -1   -1   -1
seq0020   	   -1   -1   -1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    -    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    0    0    0
seq0009   	    0    0    0
seq0013   	    0    0    0
seq0014   	    0    0    0
seq0015   	    0    0    0
seq0018   	    0    0    0
seq0020   	    0    0    0





[WARNING 'classify_msa_errors_via_mblks.2val.pl'] Somehow, NO INDELS COULDN'T BE directly ASSOCIATED to the 2nd-moved c-block for the path: (0 -> 4) !

{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 103 ,
#{columns in new reconstructed MSA} = 103 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    -    3    3
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3    -    -    -    -    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    3   -1   -1
seq0009   	    3   -1   -1
seq0013   	   -1   -1   -1
seq0014   	   -1   -1   -1
seq0015   	   -1   -1   -1
seq0018   	   -1   -1   -1
seq0020   	   -1   -1   -1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	  -68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    -    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    0    0    0
seq0009   	    0    0    0
seq0013   	    0    0    0
seq0014   	    0    0    0
seq0015   	    0    0    0
seq0018   	    0    0    0
seq0020   	    0    0    0





[WARNING 'classify_msa_errors_via_mblks.2val.pl'] Somehow, NO INDELS COULN'T BE directly ASSOCIATED to the 1st-moved c-block for the path: (4 -> 0) !


< The 2 th pair : (5, 2) >

{ The 0 th Path: (refernce ->) 5 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 103 ,
#{columns in new reconstructed MSA} = 103 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	  -68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    -    3    3
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    3   -1   -1
seq0009   	    3   -1   -1
seq0013   	   -1   -1   -1
seq0014   	   -1   -1   -1
seq0015   	   -1   -1   -1
seq0018   	   -1   -1   -1
seq0020   	   -1   -1   -1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    -    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    0    0    0
seq0009   	    0    0    0
seq0013   	    0    0    0
seq0014   	    0    0    0
seq0015   	    0    0    0
seq0018   	    0    0    0
seq0020   	    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (5 -> 2) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	2	1	0	0	0	0
2nd(reconstructed)	2	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	20:69:69:X/20:73:73:X	20:70:70:X
2nd(reconstructed)	Complex	100	20:63:65:X/20:70:70:X/21:67:68:X	20:66:70:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 2 -(intermediate)-> 5 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 103 ,
#{columns in new reconstructed MSA} = 103 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	  -68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    -    3    3
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3    -    -    -    -    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    3   -1   -1
seq0009   	    3   -1   -1
seq0013   	   -1   -1   -1
seq0014   	   -1   -1   -1
seq0015   	   -1   -1   -1
seq0018   	   -1   -1   -1
seq0020   	   -1   -1   -1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0003   	    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0008   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    -    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    -    -    -    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    0    0    0
seq0009   	    0    0    0
seq0013   	    0    0    0
seq0014   	    0    0    0
seq0015   	    0    0    0
seq0018   	    0    0    0
seq0020   	    0    0    0





[WARNING 'classify_msa_errors_via_mblks.2val.pl'] Somehow, NO INDELS COULN'T BE directly ASSOCIATED to the 1st-moved c-block for the path: (2 -> 5) !


 --- Finished analysis for the segment 5 ! ---

<<<<<< Segment ID: 6  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (13, 13)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 6 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 6 ! ---

<<<<<< Segment ID: 7  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (10, 10)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 7 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (2, 1) >

{ The 0 th Path: (refernce ->) 2 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 10 ,
#{columns in new reconstructed MSA} = 10 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9

seq0000   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0001   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0002   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0003   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0004   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0005   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0006   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0007   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0008   	    -    -    -    -    -    0    0   -1   -1    -
seq0009   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0013   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0
seq0015   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0018   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0020   	   -5   -5   -5   -5   -5    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9

seq0000   	    0    0    0    0    0    -    -    -    -    -
seq0001   	    0    0    0    0    0    -    -    -    -    -
seq0002   	    0    0    0    0    0    -    -    -    -    -
seq0003   	    0    0    0    0    0    -    -    -    -    -
seq0004   	    0    0    0    0    0    -    -    -    -    -
seq0005   	    0    0    0    0    0    -    -    -    -    -
seq0006   	    0    0    0    0    0    -    -    -    -    -
seq0007   	    0    0    0    0    0    -    -    -    -    -
seq0008   	   -5   -5   -5   -5    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    -    -    -    -    -
seq0013   	    0    0    0    0    0    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    -    -    -    -    -
seq0018   	    0    0    0    0    0    -    -    -    -    -
seq0020   	    0    0    0    0    0    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (2 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	0	1	0	0
2nd(reconstructed)	1	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	16:7:7:X	17:5:8:X
2nd(reconstructed)	Inter-branch-transfer(ref>rec)(??)	7	16:0:4:X/17:5:8:X	16:4:4:X


{Total penalty} = 107 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 10 ,
#{columns in new reconstructed MSA} = 10 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9

seq0000   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0001   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0002   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0003   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0004   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0005   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0006   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0007   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0008   	   -5   -5    -    -    -    -    -    -    0    0
seq0009   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0013   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0
seq0015   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0018   	   -5   -5   -5   -5   -5    -    -    -    -    -
seq0020   	   -5   -5   -5   -5   -5    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9

seq0000   	    0    0    0    0    0    -    -    -    -    -
seq0001   	    0    0    0    0    0    -    -    -    -    -
seq0002   	    0    0    0    0    0    -    -    -    -    -
seq0003   	    0    0    0    0    0    -    -    -    -    -
seq0004   	    0    0    0    0    0    -    -    -    -    -
seq0005   	    0    0    0    0    0    -    -    -    -    -
seq0006   	    0    0    0    0    0    -    -    -    -    -
seq0007   	    0    0    0    0    0    -    -    -    -    -
seq0008   	    0    0   -6   -6    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    -    -    -    -    -
seq0013   	    0    0    0    0    0    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    -    -    -    -    -
seq0018   	    0    0    0    0    0    -    -    -    -    -
seq0020   	    0    0    0    0    0    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 2) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	1	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	16:7:7:X	16:2:4:X
2nd(reconstructed)	Inter-branch-transfer(ref>rec)(??)	7	16:2:4:X/17:8:9:X	16:4:4:X


{Total penalty} = 107 .





 --- Finished analysis for the segment 7 ! ---

<<<<<< Segment ID: 8  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (40, 40)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 8) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 8 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (3, 4) >

{ The 0 th Path: (refernce ->) 3 -(intermediate)-> 4 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 40 ,
#{columns in new reconstructed MSA} = 40 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0005   	    0    0    -    -    -    -    -    -    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0008   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0009   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0014   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0015   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0018   	   -2   -2   -2    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1    -    -    -    -    -    4    4    4    4    4    4
seq0020   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0008   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   21   21    0    -    -    -    -    -    0    0    0    0    0    0
seq0020   	    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (3 -> 4) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	0	1	2	0	0
2nd(reconstructed)	0	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex	100	25:13:13:-	25:11:11:-/26:12:27:X
2nd(reconstructed)	Complex(???)	100	27:5:6:-	26:12:25:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 3 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 40 ,
#{columns in new reconstructed MSA} = 40 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0005   	    0    0    -    -    -    -    -    -    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0008   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0009   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0014   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0015   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0018   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   21   21   -1    -    -    -    -    -    4    4    4    4    4    4
seq0020   	   -2   -2   -2    -    -    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0008   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0020   	    0    0    0    -    -    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (4 -> 3) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	1	1	0	0	0
2nd(reconstructed)	0	0	2	2	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	25:13:13:-	26:5:25:X
2nd(reconstructed)	Complex(???)	100	25:11:13:-/26:5:25:X	25:11:11:-/26:12:25:X


{Total penalty} = 200 .





< The 2 th pair : (5, 7) >

{ The 0 th Path: (refernce ->) 5 -(intermediate)-> 7 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 40 ,
#{columns in new reconstructed MSA} = 40 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0008   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0009   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0014   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0015   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -
seq0018   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   21   21   -1    -    0    0    0    0    0    0    -    -    -    -
seq0020   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0005   	    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0008   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0009   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0014   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0015   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0018   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    -    -    4    4    4    4    4    4
seq0020   	    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    4    4    4    4    4    4





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (5 -> 7) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	17:27:27:-	17:29:29:-
2nd(reconstructed)	Merge(same-type)	2	17:29:29:-/17:36:39:-	17:29:33:-


{Total penalty} = 3 .




{ The 1 th Path: (refernce ->) 7 -(intermediate)-> 5 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 40 ,
#{columns in new reconstructed MSA} = 40 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0005   	    0    0    -    -    -    -    -    -    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0008   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0009   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0014   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0015   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4
seq0018   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   21   21   -1    -    -    -    -    -    4    4    4    4    4    4
seq0020   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    -    -    -    4    4    4    4    4    4



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0008   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    -    -    0    0    0    0    0    0
seq0020   	    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (7 -> 5) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	1	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	17:36:39:-	17:30:33:-
2nd(reconstructed)	Complex(???)	100	17:30:33:-/16:27:27:X	17:29:33:-


{Total penalty} = 101 .





 --- Finished analysis for the segment 8 ! ---

<<<<<< Segment ID: 9  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 9 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 9 ! ---

<<<<<< Segment ID: 10  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (63, 55)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 21) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 10 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (8, 5) >

{ The 0 th Path: (refernce ->) 8 -(intermediate)-> 5 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (8 -> 5) canNOT be undone completely because of the failure type, $if_success = -6: No such file or directory !

{ The 1 th Path: (refernce ->) 5 -(intermediate)-> 8 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (5 -> 8) canNOT be undone completely because of the failure type, $if_success = -13: No such file or directory !


< The 2 th pair : (15, 19) >

{ The 0 th Path: (refernce ->) 15 -(intermediate)-> 19 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (15 -> 19) canNOT be undone completely because of the failure type, $if_success = -5: No such file or directory !

{ The 1 th Path: (refernce ->) 19 -(intermediate)-> 15 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (19 -> 15) canNOT be undone completely because of the failure type, $if_success = -7: No such file or directory !


< The 3 th pair : (16, 17) >

{ The 0 th Path: (refernce ->) 16 -(intermediate)-> 17 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 63 ,
#{columns in new reconstructed MSA} = 55 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0006   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0007   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0008   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4
seq0009   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -   -4   -4   -4   -4
seq0013   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
seq0014   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    2    2    2    2    2    2    2   -7   -7   -7   -7    -    -    -   -4   -4   -4
seq0018   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3
seq0020   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	   -6   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0001   	   -6   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0002   	   -6   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0003   	   -6   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0004   	   -6   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0005   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0006   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0007   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0008   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0009   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0013   	   -7   -7   -7   -7   -7    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    0    0    -    0    0    0
seq0015   	   -4   -6   -6   -7   -7    -    -    -    -    -    -    -    -
seq0018   	   -3   -3   -6   -7   -7    -    -    -    -    -    -    -    -
seq0020   	   -3   -3   -6   -7   -7    -    -    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0
seq0020   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0



(position)	   50   51   52   53   54

seq0000   	    0    0    0    0    0
seq0001   	    0    0    0    0    0
seq0002   	    0    0    0    0    0
seq0003   	    0    0    0    0    0
seq0004   	    0    0    0    0    0
seq0005   	    0    0    0    0    0
seq0006   	    0    0    0    0    0
seq0007   	    0    0    0    0    0
seq0008   	    0    0    0    0    0
seq0009   	    0    0    0    0    0
seq0013   	    0    0    0    0    0
seq0014   	   -7   -7   -8   -8   -8
seq0015   	    0    0    0    0    0
seq0018   	    0    0    0    0    0
seq0020   	    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (16 -> 17) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	1	1	0	0
2nd(reconstructed)	1	0	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	20:59:59:-/21:62:62:-	21:50:54:X
2nd(reconstructed)	Complex(???)	100	21:57:62:-	None


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 17 -(intermediate)-> 16 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 62 ,
#{columns in new reconstructed MSA} = 55 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0006   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0007   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0008   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4
seq0009   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -   -4   -4   -4   -4
seq0013   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
seq0014   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    2    2    2    2    2    2    2   -7   -7   -7   -7    -    -    -   -4   -4   -4
seq0018   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3
seq0020   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3



(position)	   50   51   52   53   54   55   56   57   58   59   60   61

seq0000   	   -6   -6   -6    -    -    -    -    -    -    -    0    0
seq0001   	   -6   -6   -6    -    -    -    -    -    -    -    0    0
seq0002   	   -6   -6   -6    -    -    -    -    -    -    -    0    0
seq0003   	   -6   -6   -6    -    -    -    -    -    -    -    0    0
seq0004   	   -6   -6   -6    -    -    -    -    -    -    -    0    0
seq0005   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0006   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0007   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0008   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0009   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0013   	    -    -    -    -    -    -    -    0    0    0    0    0
seq0014   	   -7   -7   -8   -8   -8    -    -    -    -    -    -    -
seq0015   	   -4   -6   -6    -    -    -    -    -    -    -    0    0
seq0018   	   -3   -3   -6    -    -    -    -    -    -    -    0    0
seq0020   	   -3   -3   -6    -    -    -    -    -    -    -    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0
seq0020   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0



(position)	   50   51   52   53   54

seq0000   	    0    0    0   -7   -7
seq0001   	    0    0    0   -7   -7
seq0002   	    0    0    0   -7   -7
seq0003   	    0    0    0   -7   -7
seq0004   	    0    0    0   -7   -7
seq0005   	    0    0    0   -7   -7
seq0006   	    0    0    0   -7   -7
seq0007   	    0    0    0   -7   -7
seq0008   	    0    0    0   -7   -7
seq0009   	    0    0    0   -7   -7
seq0013   	   -7   -7   -7   -7   -7
seq0014   	    0    0    0    0    0
seq0015   	    0    0    0   -7   -7
seq0018   	    0    0    0   -7   -7
seq0020   	    0    0    0   -7   -7





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (17 -> 16) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	1	0	0
2nd(reconstructed)	1	0	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	21:62:62:-	21:53:54:-/20:50:52:X
2nd(reconstructed)	Complex(???)	100	20:57:59:-/21:60:61:X	None


{Total penalty} = 200 .





 --- Finished analysis for the segment 10 ! ---

<<<<<< Segment ID: 11  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 11 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 11 ! ---

<<<<<< Segment ID: 12  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (6, 6)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 12 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 12 ! ---

<<<<<< Segment ID: 13  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (6, 6)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 13 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 13 ! ---

<<<<<< Segment ID: 14  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (8, 8)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 14 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 14 ! ---

<<<<<< Segment ID: 15  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 15 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 15 ! ---

<<<<<< Segment ID: 16  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (49, 48)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 10) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 16 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (8, 9) >

{ The 0 th Path: (refernce ->) 8 -(intermediate)-> 9 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 49 ,
#{columns in new reconstructed MSA} = 49 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   29   29   29   29   29   29   29   29   29    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8    -    -    -    -    -    -    -    -    -    0
seq0014   	    -    1    1    0    0   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8    -    -    -    -    -    -    -    -    -    -    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0
seq0014   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -10    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (8 -> 9) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	1	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	23:46:47:X	23:38:40:X
2nd(reconstructed)	Shift	1	23:38:40:X	23:39:48:X


{Total penalty} = 101 .




{ The 1 th Path: (refernce ->) 9 -(intermediate)-> 8 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 49 ,
#{columns in new reconstructed MSA} = 49 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   29   29   29   29   29   29   29   29   29    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8    -    -    -    -    -    -    -    -    -    0
seq0014   	    -    1    1    0    0   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21    -    -    -    -    -    -    -    -    0    0    0   -2    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0
seq0014   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0   -8   -8   -8   -8    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (9 -> 8) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	1	0	0
2nd(reconstructed)	2	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	23:46:47:X	23:48:48:X/22:43:46:X
2nd(reconstructed)	Complex	100	23:35:40:X/23:48:48:X/22:43:46:X	23:39:48:X


{Total penalty} = 200 .





 --- Finished analysis for the segment 16 ! ---

<<<<<< Segment ID: 17  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 17 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 17 ! ---

<<<<<< Segment ID: 18  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (25, 24)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 18 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 25 ,
#{columns in new reconstructed MSA} = 25 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24

seq0000   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    -    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17   17
seq0013   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24

seq0000   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0001   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0002   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0003   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0004   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0005   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0006   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0007   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0008   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0013   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0014   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0015   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0018   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0020   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	1	1	0	0
2nd(reconstructed)	0	1	2	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	17:0:0:-/16:8:24:-	17:3:7:X/18:19:24:-
2nd(reconstructed)	Complex	100	16:8:18:-/17:3:7:X	18:19:19:-


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 25 ,
#{columns in new reconstructed MSA} = 25 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24

seq0000   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0001   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0002   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0003   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0004   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0005   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0006   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0007   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0008   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0014   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0015   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0018   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17
seq0020   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24

seq0000   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0001   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0002   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0003   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0004   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0005   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0006   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0007   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0008   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    -    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17   17   17
seq0013   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0014   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0015   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0018   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0020   	    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	0	1	2	0	0
2nd(reconstructed)	1	0	2	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex	100	16:8:24:-	16:8:19:-/17:20:24:X
2nd(reconstructed)	Complex	100	17:0:0:-/16:8:19:-/18:3:7:-	None


{Total penalty} = 200 .





 --- Finished analysis for the segment 18 ! ---

<<<<<< Segment ID: 19  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (15, 13)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 5) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 19 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 2) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 13 ,
#{columns in new reconstructed MSA} = 13 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12

seq0000   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0001   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0002   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0003   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0004   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0005   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0006   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0007   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0008   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0009   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0013   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0014   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0015   	    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1
seq0018   	   -2   -2    -    -    0    0    0    -    -    -    -   -2   -2
seq0020   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12

seq0000   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    -    -    -    -    -    -    4    4    4    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 2) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	26:0:1:X	26:2:3:X
2nd(reconstructed)	Merge(same-type)	2	26:2:3:X/26:7:10:X	26:2:7:X


{Total penalty} = 3 .




{ The 1 th Path: (refernce ->) 2 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 13 ,
#{columns in new reconstructed MSA} = 13 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12

seq0000   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0001   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0002   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0003   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0004   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0005   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0006   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0007   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0008   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0009   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0013   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0014   	    0    0    0    0    0    0    0    -    0   -2   -2   -2   -2
seq0015   	    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1
seq0018   	    -    -    0    0    -    -    -    -    4    4    4   -2   -2
seq0020   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12

seq0000   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	   -2   -2    -    -    -    -    -    -    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (2 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	1	1	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	28:7:7:-	26:4:7:X
2nd(reconstructed)	Merge(same-type)	2	26:0:1:X/26:4:7:X	26:2:7:X


{Total penalty} = 102 .





 --- Finished analysis for the segment 19 ! ---

<<<<<< Segment ID: 20  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (37, 36)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 20 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 20 ! ---

<<<<<< Segment ID: 21  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 21 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 21 ! ---

<<<<<< Segment ID: 22  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (17, 15)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 22 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 22 ! ---

<<<<<< Segment ID: 23  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (14, 14)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 23 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 23 ! ---

<<<<<< Segment ID: 24  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 24 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 24 ! ---

<<<<<< Segment ID: 25  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (63, 63)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 25 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 25 ! ---

<<<<<< Segment ID: 26  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 26 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 26 ! ---

<<<<<< Segment ID: 27  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 27 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 27 ! ---

<<<<<< Segment ID: 28  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 28 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 28 ! ---

<<<<<< Segment ID: 29  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 29 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 29 ! ---

<<<<<< Segment ID: 30  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (9, 9)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 30 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 30 ! ---

<<<<<< Segment ID: 31  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 31 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 31 ! ---

<<<<<< Segment ID: 32  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (25, 20)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 32 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 32 ! ---

<<<<<< Segment ID: 33  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 33 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 33 ! ---

<<<<<< Segment ID: 34  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (57, 57)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 34 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 34 ! ---

<<<<<< Segment ID: 35  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (51, 51)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 35 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 2) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 51 ,
#{columns in new reconstructed MSA} = 51 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0



(position)	   50

seq0000   	    0
seq0001   	    0
seq0002   	    0
seq0003   	    0
seq0004   	    0
seq0005   	    0
seq0006   	    0
seq0007   	    0
seq0008   	    0
seq0009   	    0
seq0013   	    2
seq0014   	    0
seq0015   	    0
seq0018   	    0
seq0020   	    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36    0    0



(position)	   50

seq0000   	    0
seq0001   	    0
seq0002   	    0
seq0003   	    0
seq0004   	    0
seq0005   	    0
seq0006   	    0
seq0007   	    0
seq0008   	    0
seq0009   	    0
seq0013   	    0
seq0014   	    0
seq0015   	    0
seq0018   	    0
seq0020   	    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 2) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	27:0:0:-	27:8:8:-
2nd(reconstructed)	Merge(same-type)	2	27:8:8:-/27:12:47:-	27:8:44:-


{Total penalty} = 3 .




{ The 1 th Path: (refernce ->) 2 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 51 ,
#{columns in new reconstructed MSA} = 51 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36    0    0



(position)	   50

seq0000   	    0
seq0001   	    0
seq0002   	    0
seq0003   	    0
seq0004   	    0
seq0005   	    0
seq0006   	    0
seq0007   	    0
seq0008   	    0
seq0009   	    0
seq0013   	    2
seq0014   	    0
seq0015   	    0
seq0018   	    0
seq0020   	    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0



(position)	   50

seq0000   	    0
seq0001   	    0
seq0002   	    0
seq0003   	    0
seq0004   	    0
seq0005   	    0
seq0006   	    0
seq0007   	    0
seq0008   	    0
seq0009   	    0
seq0013   	    0
seq0014   	    0
seq0015   	    0
seq0018   	    0
seq0020   	    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (2 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	27:12:47:-	27:9:44:-
2nd(reconstructed)	Merge(same-type)	2	27:0:0:-/27:9:44:-	27:8:44:-


{Total penalty} = 3 .





 --- Finished analysis for the segment 35 ! ---

<<<<<< Segment ID: 36  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 36 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 36 ! ---

<<<<<< Segment ID: 37  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 37 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 37 ! ---

<<<<<< Segment ID: 38  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (41, 34)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 38 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 38 ! ---

<<<<<< Segment ID: 39  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 39 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 39 ! ---

<<<<<< Segment ID: 40  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (36, 36)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 40 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 40 ! ---

<<<<<< Segment ID: 41  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 41 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 41 ! ---

<<<<<< Segment ID: 42  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 1)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 42 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 42 ! ---

<<<<<< Segment ID: 43  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (11, 8)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 43 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 43 ! ---

<<<<<< Segment ID: 44  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (7, 5)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 44 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 5 ,
#{columns in new reconstructed MSA} = 5 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4

seq0000   	    0    -    -    -    0
seq0001   	    0    -    -    -    0
seq0002   	    0    -    -    -    0
seq0003   	    0    -    -    -    0
seq0004   	    0    -    -    -    0
seq0005   	    0    -    -    -    0
seq0006   	    0    -    -    -    0
seq0007   	    0    -    -    -    0
seq0008   	    0    -    -    -    0
seq0009   	    0    -    -    -    0
seq0013   	    0    -   -2   -2   -2
seq0014   	    0    0    0    0    0
seq0015   	    0    -    -    -    0
seq0018   	    0    -    -    -    0
seq0020   	    0    -    -    -    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4

seq0000   	    -    -    -    3    0
seq0001   	    -    -    -    3    0
seq0002   	    -    -    -    3    0
seq0003   	    -    -    -    3    0
seq0004   	    -    -    -    3    0
seq0005   	    -    -    -    3    0
seq0006   	    -    -    -    3    0
seq0007   	    -    -    -    3    0
seq0008   	    -    -    -    3    0
seq0009   	    -    -    -    3    0
seq0013   	    0    -    0    0    0
seq0014   	    0    0    0    0    0
seq0015   	    -    -    -    3    0
seq0018   	    -    -    -    3    0
seq0020   	    -    -    -    3    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	1	2	0	0
2nd(reconstructed)	0	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Partial-Neighboring-Branch-Merge(2ins)(+shift)(?)	6	20:5:6:-/21:1:3:-	21:1:1:-/22:2:3:-
2nd(reconstructed)	Complex(???)	100	None	22:0:2:-


{Total penalty} = 106 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 7 ,
#{columns in new reconstructed MSA} = 5 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6

seq0000   	    -    -    -    3    0    -    -
seq0001   	    -    -    -    3    0    -    -
seq0002   	    -    -    -    3    0    -    -
seq0003   	    -    -    -    3    0    -    -
seq0004   	    -    -    -    3    0    -    -
seq0005   	    -    -    -    3    0    -    -
seq0006   	    -    -    -    3    0    -    -
seq0007   	    -    -    -    3    0    -    -
seq0008   	    -    -    -    3    0    -    -
seq0009   	    -    -    -    3    0    -    -
seq0013   	    0    -    -    -    0    0    0
seq0014   	    0    0    0    0    0    -    -
seq0015   	    -    -    -    3    0    -    -
seq0018   	    -    -    -    3    0    -    -
seq0020   	    -    -    -    3    0    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4

seq0000   	    -    -    -    0    0
seq0001   	    -    -    -    0    0
seq0002   	    -    -    -    0    0
seq0003   	    -    -    -    0    0
seq0004   	    -    -    -    0    0
seq0005   	    -    -    -    0    0
seq0006   	    -    -    -    0    0
seq0007   	    -    -    -    0    0
seq0008   	    -    -    -    0    0
seq0009   	    -    -    -    0    0
seq0013   	    0    -   -2   -2   -2
seq0014   	    0    0    0    0    0
seq0015   	    -    -    -    0    0
seq0018   	    -    -    -    0    0
seq0020   	    -    -    -    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	0	1	2	0	0
2nd(reconstructed)	2	0	0	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex	100	21:1:3:-	21:1:2:-/20:3:3:X
2nd(reconstructed)	Complex	100	20:3:3:X/20:5:6:-	21:1:1:-


{Total penalty} = 200 .





 --- Finished analysis for the segment 44 ! ---

<<<<<< Segment ID: 45  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (63, 51)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 45 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (3, 1) >

{ The 0 th Path: (refernce ->) 3 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 63 ,
#{columns in new reconstructed MSA} = 63 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0002   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0006   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0007   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0008   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0020   	    0    -    -    -    -    -    -    -    -    -    -    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -   12    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0002   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0006   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0007   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0008   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0020   	   12   12   12   12   12   12   12   12   12   12   12   12   12





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (3 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	0	1	0	2
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	16	28:1:50:-/23:54:56:-	26:16:18:X/19:16:18:X/22:16:18:X
2nd(reconstructed)	Complex(???)	100	28:19:50:-/28:1:12:-	28:19:56:-


{Total penalty} = 116 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 3 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 63 ,
#{columns in new reconstructed MSA} = 63 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -   12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0002   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0003   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0004   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0005   	    -    0    0    0    -    -    -    0    0    0    0    0    -
seq0006   	    -    0    0    0    -    -    -    0    0    0    0    0    -
seq0007   	    -    0    0    0    -    -    -    0    0    0    0    0    -
seq0008   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0009   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0013   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0014   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0015   	    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    -    0    0    0    -    -    -    0    0    0    0    0    0
seq0020   	   12   12   12   12   12   12   12   12   12   12   12   12   12



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    0  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0002   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0006   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0007   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0008   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0





[WARNING 'classify_msa_errors_via_mblks.2val.pl'] Somehow, NO INDELS COULDN'T BE directly ASSOCIATED to the 2nd-moved c-block for the path: (1 -> 3) !


 --- Finished analysis for the segment 45 ! ---

<<<<<< Segment ID: 46  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (3, 3)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 46 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 46 ! ---



 === All the Analyses FINISHED !! ===

#{Segments skipped} = 2 .
#{Segments whose ComplLiMMent calculations skipped} = 0 .
#{Anomalous segments} = 0 .
#{Segments used as inputs} = 0 .
#{Segments successfully processed} = 45 .
#{Segments failed to be processed} = 0 .


real	0m2.234s
user	0m1.120s
sys	0m0.666s
