[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_PRANK/class_0001/lclid_0000003 .

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_PRANK/Temporary/class_0001/dawg_inp0000003.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_PRANK/Temporary/class_0001/refaln.0000003.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_PRANK/Temporary/class_0001/dawg_inp0000003.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_PRANK/Temporary/class_0001/refaln.0000003.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_PRANK/Temporary/class_0001/recaln.0000003.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_PRANK/Temporary/class_0001/equiv_rgs_brief.0000003.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} = 41

Seg_ID	Start_in_Ref	End_in_ref	Start_in_Rec	End_in_Rec	Diagnosis

0	0	24	0	24	CLEARLY_DIFFERENT
1	27	41	27	41	CLEARLY_DIFFERENT
2	43	55	43	55	CLEARLY_DIFFERENT
3	68	83	68	82	CLEARLY_DIFFERENT
4	172	175	171	174	CLEARLY_DIFFERENT
5	186	272	185	268	CLEARLY_DIFFERENT
6	281	294	277	292	CLEARLY_DIFFERENT
7	331	337	329	335	CLEARLY_DIFFERENT
8	342	365	340	362	CLEARLY_DIFFERENT
9	374	593	371	589	CLEARLY_DIFFERENT
10	651	656	647	652	CLEARLY_DIFFERENT
11	667	669	663	665	CLEARLY_DIFFERENT
12	687	689	683	685	CLEARLY_DIFFERENT
13	690	698	686	695	CLEARLY_DIFFERENT
14	704	711	701	708	CLEARLY_DIFFERENT
15	713	738	710	735	CLEARLY_DIFFERENT
16	747	754	744	751	CLEARLY_DIFFERENT
17	769	810	766	807	CLEARLY_DIFFERENT
18	821	828	818	825	CLEARLY_DIFFERENT
19	831	836	828	833	CLEARLY_DIFFERENT
20	838	840	835	837	CLEARLY_DIFFERENT
21	849	912	846	906	CLEARLY_DIFFERENT
22	913	915	907	909	CLEARLY_DIFFERENT
23	916	942	910	939	CLEARLY_DIFFERENT
24	968	1048	965	1042	CLEARLY_DIFFERENT
25	1057	1064	1051	1057	CLEARLY_DIFFERENT
26	1079	1085	1072	1078	CLEARLY_DIFFERENT
27	1088	1150	1081	1142	CLEARLY_DIFFERENT
28	1156	1161	1148	1153	CLEARLY_DIFFERENT
29	1167	1182	1159	1174	CLEARLY_DIFFERENT
30	1191	1218	1183	1207	CLEARLY_DIFFERENT
31	1228	1230	1217	1219	CLEARLY_DIFFERENT
32	1234	1243	1223	1232	CLEARLY_DIFFERENT
33	1247	1252	1236	1241	CLEARLY_DIFFERENT
34	1253	1289	1242	1278	CLEARLY_DIFFERENT
35	1296	1389	1285	1357	CLEARLY_DIFFERENT
36	1403	1420	1371	1388	CLEARLY_DIFFERENT
37	1469	1476	1437	1443	CLEARLY_DIFFERENT
38	1485	1506	1452	1473	CLEARLY_DIFFERENT
39	1519	1523	1486	1490	CLEARLY_DIFFERENT
40	1543	1543	1510	1510	IDENTICAL



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

#{sequences in MSA} =  15 .
#{columns in MSA}   = 1543 .


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

#{columns in MSA} = 1510 .


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

#{columns in MSA} = 1543 .


<<<<< 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: 0  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (24, 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} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 0 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, 0) >

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 24 ,
#{columns in new reconstructed MSA} = 24 .

$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

seq0000   	    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
seq0002   	    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
seq0004   	    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
seq0006   	    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
seq0008   	    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
seq0013   	    0    0    0    0    0    0    0    -    -    -    -    -    -    6    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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -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   17   18   19   20   21   22   23

seq0000   	    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
seq0002   	    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
seq0004   	    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
seq0006   	    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
seq0008   	    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
seq0013   	    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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0
seq0018   	    -    1    1    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    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 -> 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	2	0	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)	Split(same-type)	2	27:0:18:-	27:0:7:-/27:18:23:-
2nd(reconstructed)	Complex(???)	100	25:2:2:-/27:0:7:-	25:0:0:-/27:1:7:-


{Total penalty} = 102 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 24 ,
#{columns in new reconstructed MSA} = 24 .

$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

seq0000   	    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
seq0002   	    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
seq0004   	    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
seq0006   	    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
seq0008   	    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
seq0013   	    0    0    0    0    0    0    0    -    -    -    -    -    -    6    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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0
seq0018   	    -    1    1    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

seq0000   	    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
seq0002   	    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
seq0004   	    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
seq0006   	    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
seq0008   	    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
seq0013   	    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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6    -    -    -    -    -    -





[ 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)	0	0	2	2	0	0
2nd(reconstructed)	1	2	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	25:2:2:-/27:0:18:-	25:0:0:-/27:1:18:-
2nd(reconstructed)	Split(same-type)	2	27:1:18:-	27:1:7:-/27:18:23:-


{Total penalty} = 102 .





 --- Finished analysis for the segment 0 ! ---

<<<<<< Segment ID: 1  (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 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 ... >>


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

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

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

(ref_len, rec_len) = (12, 12)

<<<<< 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) = (15, 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} = 5) >>>>>


... 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 ... >>


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

<<<<<< Segment ID: 4  (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 4 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 4 ! ---

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

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

(ref_len, rec_len) = (86, 83)

<<<<< 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} = 23) >>>>>


... 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 : (3, 1) >

{ The 0 th Path: (refernce ->) 3 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 86 ,
#{columns in new reconstructed MSA} = 86 .

$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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0001   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0005   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0006   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0007   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0008   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    -    0    0    0    0
seq0009   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    -    -    -   -3   -3   -3   -3   -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
seq0014   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    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    0    -    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    3    3    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -   11    0    0    0    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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    1    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

seq0000   	    0    -    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    -    -    2    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   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
seq0001   	    -    -    -    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
seq0003   	    -    -    -    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
seq0005   	    -    -    -    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
seq0007   	    -    -    -    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
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
seq0013   	    -    -    -    3    3    3    3    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    -    -    -    -    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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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



(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

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
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
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    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    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
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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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





[ 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)	2	2	0	0	0	0
2nd(reconstructed)	2	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	20:7:12:X/20:16:16:-	20:7:9:X/20:17:19:X
2nd(reconstructed)	Purge(?)	3	20:7:9:X/20:0:2:-	None


{Total penalty} = 103 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 86 ,
#{columns in new reconstructed MSA} = 86 .

$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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0001   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0005   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0006   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0007   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0008   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    -    0    0    0    0
seq0009   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    3    3    3    3    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    -    -    -    -    0    0    -    0    0    0    0
seq0014   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    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    0    -    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    3    3    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -   11    0    0    0    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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    1    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

seq0000   	    0    -    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    -    -    2    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   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
seq0001   	    -    -    -    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
seq0003   	    -    -    -    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
seq0005   	    -    -    -    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
seq0007   	    -    -    -    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
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
seq0013   	    -    -    -    0    0    0    0    0    0    0   -3   -3   -3   -3   -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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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



(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

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
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
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    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    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
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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 3) ]

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	20:7:12:X	20:10:12:X
2nd(reconstructed)	Shift	1	20:10:12:X	20:17:19:X


{Total penalty} = 101 .





< The 2 th pair : (10, 2) >

{ The 0 th Path: (refernce ->) 10 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 86 ,
#{columns in new reconstructed MSA} = 86 .

$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    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    -    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    3    3    3    3    3    3    3   -3   -3   -3   -3   -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
seq0014   	    0    0    0    0    0    0    0    0    0    -    -    -    1    1    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    0    -    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -   11    0    0    0    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    -    -    -    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    1    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

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

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
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
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    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    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
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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (10 -> 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)	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	26:11:21:X/26:9:10:-	26:12:20:X
2nd(reconstructed)	Complex(???)	100	26:12:20:X/27:9:9:-	26:13:20:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 2 -(intermediate)-> 10 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 86 ,
#{columns in new reconstructed MSA} = 86 .

$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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0001   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0005   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0006   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0007   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0008   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    -    0    0    0    0
seq0009   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    3    3    3    3    3    3    3   -3   -3   -3   -3   -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
seq0014   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    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    0    -    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    3    3    3    3    3    3    3    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    0
seq0020   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    1    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

seq0000   	    0    -    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    -    -    2    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   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
seq0001   	    -    -    -    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
seq0003   	    -    -    -    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
seq0005   	    -    -    -    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
seq0007   	    -    -    -    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
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
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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    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



(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

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
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
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    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    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
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
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
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (2 -> 10) ]

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(complementary)	2	26:11:21:X/26:9:10:-	26:14:21:X
2nd(reconstructed)	Shift	1	26:14:21:X	26:13:20:X


{Total penalty} = 3 .





< The 3 th pair : (17, 4) >

{ The 0 th Path: (refernce ->) 17 -(intermediate)-> 4 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (17 -> 4) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !

{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 17 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (4 -> 17) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


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

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

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

(ref_len, rec_len) = (13, 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} = 4) >>>>>


... 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) = (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} = 1) >>>>>


... 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 ... >>


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

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

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

(ref_len, rec_len) = (23, 22)

<<<<< 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 : (2, 0) >

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

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

$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    -    1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    -    0    0    0    -    1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    -    0    0    0    -    1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    -    0    0    0    -    1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    -    0    0    0    -    1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0006   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0007   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0008   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0009   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    -    0    0    0
seq0013   	    -    -    -    3    3    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0014   	    0    -    0    0    0    -    1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    -    0    0    0    -    1    0    0    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0018   	    0    -    0    0    0    0    0   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    0    0
seq0020   	    0    -    0   -1    -    -    1   -1    -    0    0    0    0    0   -2    -    -    0    0    0    0    -    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

seq0000   	    -    1    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    1    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    1    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    1    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    1    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    1    0    0    0    -    0    0    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0006   	    -    1    0    0    0    -    0    0    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0007   	    -    1    0    0    0    -    0    0    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0008   	    -    1    0    0    0    -    0    0    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0009   	    -    1    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
seq0014   	    -    1    0    0    0    -    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    1    0    0    0    -    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0018   	    -    1    0    0    0    0    0    0    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0020   	    -    1    0    0    -    -    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: (2 -> 0) !

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

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

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

seq0000   	    -    0    0    0    0    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    0    0    0    0    -    0    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    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
seq0007   	    -    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
seq0009   	    -    0    0    0    0    -    0    0    -    0    0    0    0    0    0    -    -    0    0    -    0    0    0
seq0013   	    -    -    -    3    3    -    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
seq0015   	    -    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
seq0020   	    -    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 (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	20:1:1:-	20:0:0:-
2nd(reconstructed)	Merge(complementary)(+shift)(?)	3	20:2:4:X/20:0:0:-	20:1:2:X


{Total penalty} = 4 .





< The 2 th pair : (3, 1) >

{ The 0 th Path: (refernce ->) 3 -(intermediate)-> 1 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 1) has a NON-POSITIVE left-end shift (=0) and a NON-NEGATIVE right-end shift (=0): No such file or directory !


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (3 -> 1) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !

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

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The new 1st moved c-block (index: 1) became EMPTY in the intermediate MSA: No such file or directory !


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (1 -> 3) canNOT be undone completely because of the failure type, $if_success = -105: No such file or directory !


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

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

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

(ref_len, rec_len) = (219, 218)

<<<<< 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 a cluster of length 209, which is LONGER THAN the upper-bound, 150... I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 9 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


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

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

(ref_len, rec_len) = (5, 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 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 ... >>


 --- 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) = (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 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) = (8, 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} = 4) >>>>>


... 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) = (7, 7)

<<<<< 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 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) = (25, 25)

<<<<< 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 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) = (7, 7)

<<<<< 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 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 ... >>


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

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

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

(ref_len, rec_len) = (41, 41)

<<<<< 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) = (7, 7)

<<<<< 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 ... >>


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

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

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

(ref_len, rec_len) = (5, 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} = 1) >>>>>


... 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 ... >>


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

<<<<<< Segment ID: 20  (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 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) = (63, 60)

<<<<< 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} = 9) >>>>>


... 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 ... >>


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

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


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (3 -> 4) canNOT be undone completely because of the failure type, $if_success = -5: No such file or directory !

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


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (4 -> 3) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


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

<<<<<< Segment ID: 22  (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 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) = (26, 29)

<<<<< 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 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 ... >>


< The 1 th pair : (4, 7) >

{ The 0 th Path: (refernce ->) 4 -(intermediate)-> 7 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (4 -> 7) canNOT be undone completely because of the failure type, $if_success = -7: No such file or directory !

{ The 1 th Path: (refernce ->) 7 -(intermediate)-> 4 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (7 -> 4) canNOT be undone completely because of the failure type, $if_success = -2: No such file or directory !


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

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

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

(ref_len, rec_len) = (80, 77)

<<<<< 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} = 18) >>>>>


... 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 ... >>


< The 1 th pair : (0, 5) >

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 80 ,
#{columns in new reconstructed MSA} = 80 .

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



(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

seq0000   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0001   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0002   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0003   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0004   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0006   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0007   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0008   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0
seq0009   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0013   	    -    -    4    4    2    2    2    2    2    2    2    2    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    -    1
seq0014   	    -    -    -    -    -    -    -    -    -   43   43   43   43    -    -   45   45    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0015   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0018   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48    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   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
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
seq0002   	    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    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
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
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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

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    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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 5) ]

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	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	8:15:15:X/8:0:14:-	8:1:16:-
2nd(reconstructed)	Merge(complementary)	2	8:32:33:X/8:1:16:-	8:3:16:-


{Total penalty} = 102 .




{ The 1 th Path: (refernce ->) 5 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 80 ,
#{columns in new reconstructed MSA} = 80 .

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



(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

seq0000   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0001   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0002   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0003   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0004   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0006   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0007   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0008   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0
seq0009   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0013   	    -    -    4    4    2    2    2    2    2    2    2    2    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    -    1
seq0014   	    -    -    -    -    -    -    -    -    -   43   43   43   43    -    -   45   45    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0015   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0018   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48    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   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
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
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    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    0    0    0
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    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    0    0    0
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    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    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
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
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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

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    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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    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: (5 -> 0) !


< The 2 th pair : (16, 4) >

{ The 0 th Path: (refernce ->) 16 -(intermediate)-> 4 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 80 ,
#{columns in new reconstructed MSA} = 80 .

$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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

seq0000   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0001   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0002   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0003   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0004   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0006   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0007   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0008   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0
seq0009   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0013   	    -    -    4    4    2    2    2    2    2    2    2    2    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    -    1
seq0014   	    -    -    -    -    -    -    -    -    -   43   43   43   43    -    -   45   45    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0015   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0018   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48    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   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
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
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
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
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
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
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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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

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    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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (16 -> 4) ]

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	27:29:76:-	27:28:75:-
2nd(reconstructed)	Complex(???)	100	27:28:75:-/26:15:16:X	27:30:75:-


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 16 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 80 ,
#{columns in new reconstructed MSA} = 80 .

$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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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

seq0000   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0001   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0002   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0003   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0004   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0006   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0007   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0008   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0
seq0009   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0013   	    -    -    4    4    2    2    2    2    2    2    2    2    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    -    1
seq0014   	    -    -    -    -    -    -    -    -    -   43   43   43   43    -    -   45   45    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0015   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0018   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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   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
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
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
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
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
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
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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

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    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
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
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
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
seq0014   	    -    -    -    -    -    -    -    -    -    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
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
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   46    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (4 -> 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	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)	Shift(???)	2	27:29:76:-	27:31:76:-
2nd(reconstructed)	Shift	1	27:31:76:-	27:30:75:-


{Total penalty} = 3 .





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

<<<<<< Segment ID: 25  (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} = 1) >>>>>


... 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) = (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} = 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) = (62, 61)

<<<<< 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} = 6) >>>>>


... 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) = (5, 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} = 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) = (15, 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} = 1) >>>>>


... 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) = (27, 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} = 7) >>>>>


... 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 ... >>


< The 1 th pair : (2, 4) >

{ The 0 th Path: (refernce ->) 2 -(intermediate)-> 4 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (2 -> 4) canNOT be undone completely because of the failure type, $if_success = -2: No such file or directory !

{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 2 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (4 -> 2) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


 --- Finished analysis for the segment 30 ! ---

<<<<<< Segment ID: 31  (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 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) = (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 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) = (5, 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} = 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) = (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} = 5) >>>>>


... 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) = (93, 72)

<<<<< 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} = 17) >>>>>


... 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 ... >>


 --- Finished analysis for the segment 35 ! ---

<<<<<< Segment ID: 36  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (17, 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} = 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) = (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 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 ... >>


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

{ The 0 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} = 7 .

$baseline_shift_intm = 0 .

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

(position)	    0    1    2    3    4    5    6

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   	    -    1    1    1    1    1    1
seq0014   	    -    -    0    0    0    0    0
seq0015   	    -    -    0    0    0    0    0
seq0018   	    -    -    0    0    0    0    0
seq0020   	    -    -    0    0    0    0    0



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

(position)	    0    1    2    3    4    5    6

seq0000   	    -   -1    -    0    0    0    0
seq0001   	    -   -1    -    0    0    0    0
seq0002   	    -   -1    -    0    0    0    0
seq0003   	    -   -1    -    0    0    0    0
seq0004   	    -   -1    -    0    0    0    0
seq0005   	    -   -1    -    0    0    0    0
seq0006   	    -   -1    -    0    0    0    0
seq0007   	    -   -1    -    0    0    0    0
seq0008   	    -   -1    -    0    0    0    0
seq0009   	    -   -1    -    0    0    0    0
seq0013   	    -    0    0    0    0    0    0
seq0014   	    -   -1    -    0    0    0    0
seq0015   	    -   -1    -    0    0    0    0
seq0018   	    -   -1    -    0    0    0    0
seq0020   	    -   -1    -    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(complementary)	2	20:6:6:X/20:0:1:-	20:1:1:-
2nd(reconstructed)	Shift	1	20:1:1:-	20:2:2:-


{Total penalty} = 3 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 7 ,
#{columns in new reconstructed MSA} = 7 .

$baseline_shift_intm = 0 .

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

(position)	    0    1    2    3    4    5    6

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



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

(position)	    0    1    2    3    4    5    6

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   	    -    1    1    1    1    1    1
seq0014   	    -    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 (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	2	0	0	0	0
2nd(reconstructed)	3	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)	Split(same-type)	2	20:0:1:-	20:0:0:-/20:2:2:-
2nd(reconstructed)	Complex	100	20:6:6:X/20:0:0:-/20:2:2:-	20:2:2:-


{Total penalty} = 102 .





 --- Finished analysis for the segment 37 ! ---

<<<<<< Segment ID: 38  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (21, 21)

<<<<< 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 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 ! ---



 === All the Analyses FINISHED !! ===

#{Segments skipped} = 1 .
#{Segments whose ComplLiMMent calculations skipped} = 0 .
#{Anomalous segments} = 0 .
#{Segments used as inputs} = 0 .
#{Segments successfully processed} = 39 .
#{Segments failed to be processed} = 0 .


real	0m2.121s
user	0m1.119s
sys	0m0.604s
