[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_0000001 .

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_inp0000001.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.0000001.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_inp0000001.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.0000001.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.0000001.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.0000001.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} = 37

Seg_ID	Start_in_Ref	End_in_ref	Start_in_Rec	End_in_Rec	Diagnosis

0	0	14	0	15	CLEARLY_DIFFERENT
1	28	30	29	31	CLEARLY_DIFFERENT
2	31	33	32	34	CLEARLY_DIFFERENT
3	47	144	48	144	CLEARLY_DIFFERENT
4	152	155	152	155	CLEARLY_DIFFERENT
5	156	656	156	597	CLEARLY_DIFFERENT
6	666	695	607	636	CLEARLY_DIFFERENT
7	696	704	637	644	CLEARLY_DIFFERENT
8	715	718	655	658	CLEARLY_DIFFERENT
9	729	731	669	671	CLEARLY_DIFFERENT
10	732	805	672	728	CLEARLY_DIFFERENT
11	825	836	748	760	CLEARLY_DIFFERENT
12	844	846	768	770	CLEARLY_DIFFERENT
13	869	879	793	803	CLEARLY_DIFFERENT
14	886	932	810	856	CLEARLY_DIFFERENT
15	978	986	902	910	CLEARLY_DIFFERENT
16	993	1198	917	1080	CLEARLY_DIFFERENT
17	1211	1214	1093	1096	CLEARLY_DIFFERENT
18	1254	1325	1136	1204	CLEARLY_DIFFERENT
19	1362	1365	1241	1244	CLEARLY_DIFFERENT
20	1368	1412	1247	1293	CLEARLY_DIFFERENT
21	1428	1460	1309	1341	CLEARLY_DIFFERENT
22	1466	1521	1347	1404	CLEARLY_DIFFERENT
23	1526	1529	1409	1411	CLEARLY_DIFFERENT
24	1530	1533	1412	1415	CLEARLY_DIFFERENT
25	1538	1545	1420	1427	CLEARLY_DIFFERENT
26	1559	1583	1441	1463	CLEARLY_DIFFERENT
27	1587	1596	1467	1475	CLEARLY_DIFFERENT
28	1614	1632	1493	1511	CLEARLY_DIFFERENT
29	1638	1654	1517	1532	CLEARLY_DIFFERENT
30	1673	1690	1551	1567	CLEARLY_DIFFERENT
31	1696	1699	1573	1576	CLEARLY_DIFFERENT
32	1714	1718	1591	1595	CLEARLY_DIFFERENT
33	1723	1725	1600	1602	CLEARLY_DIFFERENT
34	1727	1736	1604	1613	CLEARLY_DIFFERENT
35	1738	1740	1615	1617	CLEARLY_DIFFERENT
36	1752	1826	1629	1703	CLEARLY_DIFFERENT



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

#{sequences in MSA} =  15 .
#{columns in MSA}   = 1826 .


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

#{columns in MSA} = 1703 .


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

#{columns in MSA} = 1826 .


<<<<< 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) = (14, 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} = 6) >>>>>


... 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, 1) >

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 15 ,
#{columns in new reconstructed MSA} = 15 .

$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

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

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





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

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

1st(intermediate)	1	2	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	23:13:13:X	23:3:6:X/23:11:11:-
2nd(reconstructed)	Complex(???)	100	23:3:6:X/22:0:1:X	23:5:6:X


{Total penalty} = 200 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 15 ,
#{columns in new reconstructed MSA} = 15 .

$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

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

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





[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: (1 -> 2) !


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

<<<<<< Segment ID: 1  (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 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) = (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 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) = (97, 96)

<<<<< 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 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) = (500, 441)

<<<<< 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 190, 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 5 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


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

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

(ref_len, rec_len) = (29, 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} = 1) >>>>>


... 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) = (8, 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 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) = (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 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 ... >>


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

<<<<<< Segment ID: 9  (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 9 th segment ...


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


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


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

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

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

(ref_len, rec_len) = (73, 56)

<<<<< 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} = 12) >>>>>


... 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) = (11, 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} = 3) >>>>>


... 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) = (10, 10)

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

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

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

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

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

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

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

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

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

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

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

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


... 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) = (46, 46)

<<<<< 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 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 ... >>


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 46 ,
#{columns in new reconstructed MSA} = 46 .

$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

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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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
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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    0    0    0    0    0    -    -   -1   -1   -1   -1    -    0
seq0013   	    -    1    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    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   -1    -    -    -    -    -    -    -    6    6    6    6    6    6    6    6    3    3    3    3    3    3    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    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    -    -    -    3    3    3    3    3    3    3    -    -    5    -    -    -    8    8
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    -    -    -    3    3    0    0    0    0    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   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
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
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
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
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seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
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seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    -    -
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seq0013   	    -    0   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7    -    -    -    -    -    -    -    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
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
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    -





[ 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)	1	0	1	1	0	0


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

1st(intermediate)	Split(same-type)	2	20:1:8:X	20:0:0:X/20:2:8:X
2nd(reconstructed)	Neighboring-branch-Merge(2del)(?)	4	20:2:8:X/21:12:18:X	22:12:18:X


{Total penalty} = 6 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 46 ,
#{columns in new reconstructed MSA} = 46 .

$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

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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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
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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    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    -    -    -    3    3    0    0    0    0    0    -    -   -1   -1   -1   -1    -    0
seq0013   	    0    -   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3    3    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   -1    -    -    -    -    -    -    -    6    6    6    6    6    6    6    6    3    3    3    3    3    3    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    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    -    -    -    3    3    3    3    3    3    3    -    -    5    -    -    -    8    8
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    -    -    -    3    3    0    0    0    0    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   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
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
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
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
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    -    0
seq0013   	    -    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    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
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
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    -





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

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

1st(intermediate)	1	1	0	1	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	20:1:8:X	20:1:1:X/22:12:18:X
2nd(reconstructed)	Shift	1	20:1:1:X	20:0:0:X


{Total penalty} = 101 .





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

{ The 0 th Path: (refernce ->) 2 -(intermediate)-> 3 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (2 -> 3) canNOT be undone completely because of the failure type, $if_success = -7: No such file or directory !

{ The 1 th Path: (refernce ->) 3 -(intermediate)-> 2 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 2) has a NON-POSITIVE left-end shift (=-1) and a NON-NEGATIVE right-end shift (=6): 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 (3 -> 2) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !


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

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

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

(ref_len, rec_len) = (8, 8)

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

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

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

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

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

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

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

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

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

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

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

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... 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) = (205, 163)

<<<<< 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} = 31) >>>>>


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


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


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


< The 1 th pair : (12, 16) >

{ The 0 th Path: (refernce ->) 12 -(intermediate)-> 16 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 16) 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 (12 -> 16) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !

{ The 1 th Path: (refernce ->) 16 -(intermediate)-> 12 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (16 -> 12) canNOT be undone completely because of the failure type, $if_success = -2: No such file or directory !


< The 2 th pair : (19, 23) >

{ The 0 th Path: (refernce ->) 19 -(intermediate)-> 23 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (19 -> 23) canNOT be undone completely because of the failure type, $if_success = -13: No such file or directory !

{ The 1 th Path: (refernce ->) 23 -(intermediate)-> 19 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (23 -> 19) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


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

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

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

(ref_len, rec_len) = (3, 3)

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (71, 68)

<<<<< 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 18 th segment ...


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


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


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

{ The 0 th Path: (refernce ->) 2 -(intermediate)-> 3 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 71 ,
#{columns in new reconstructed MSA} = 71 .

$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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0001   	    -    -    -    3   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0002   	    -    -    -    3   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    3   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    -    -    -   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    3   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    3   -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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    3   -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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    3   -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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   14   -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
seq0009   	    -    -    -    3    3    -    -    -    -    -    -    -    -   11   11   11    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    3    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    3    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    3    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    3    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70

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



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

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

seq0000   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0001   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
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
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
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
seq0005   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
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
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  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    0  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    0  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    0  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    0  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70

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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (2 -> 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	1	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	15:5:15:-	15:5:12:-/19:4:15:-
2nd(reconstructed)	Complex(???)	100	19:4:15:-/19:17:69:-	None


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 3 -(intermediate)-> 2 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 71 ,
#{columns in new reconstructed MSA} = 71 .

$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    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0001   	    -    -    -    3    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0002   	    -    -    -    3    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    3    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    3    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    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    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   14   -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
seq0009   	    -    -    -    3    3    -    -    -    -    -    -    -    -   11   11   11    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    3  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    3  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    3  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    3  -12    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70

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



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

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

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



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70

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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (3 -> 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	0	1	2	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	19:17:69:-/15:5:15:-	15:5:12:-/15:4:4:X
2nd(reconstructed)	Complex(???)	100	15:4:4:X/15:5:12:-	15:5:12:-


{Total penalty} = 200 .





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

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

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

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


... 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) = (44, 46)

<<<<< 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 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 ... >>


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 46 ,
#{columns in new reconstructed MSA} = 46 .

$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

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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    0    -    -    -    0    0    0    0    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    2    0    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    2    2    2    2    2
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -
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    -    -    -
seq0020   	    -    -    -    3    3    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    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    -    -    -
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
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -
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    -    -    -
seq0020   	    -    -    -    0    0  -35  -35    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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)	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)	Split(same-type)	2	27:2:39:-	27:0:2:-/27:5:39:-
2nd(reconstructed)	Shift	1	27:5:39:-	27:7:41:-


{Total penalty} = 3 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 46 ,
#{columns in new reconstructed MSA} = 46 .

$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

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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    0    -    -    -    0    0    0    0    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    2    0    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    2    2    2    2    2
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -
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    -    -    -
seq0020   	    0    0    -    -    -  -35  -35    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    -    -    -
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    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    -    -    -
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
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -
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    -    -    -
seq0020   	    -    -    -    3    3    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -





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

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

1st(intermediate)	1	2	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)	Split(same-type)	2	27:2:39:-	27:2:4:-/27:7:41:-
2nd(reconstructed)	Shift	1	27:2:4:-	27:0:2:-


{Total penalty} = 3 .





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

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

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

(ref_len, rec_len) = (32, 32)

<<<<< 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 21 th segment ...


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


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


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

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

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

(ref_len, rec_len) = (55, 57)

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

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

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

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

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

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

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

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

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

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

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

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 16) >>>>>


... 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 ... >>


< The 1 th pair : (0, 3) >

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


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

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


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (3 -> 0) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


< The 2 th pair : (10, 9) >

{ The 0 th Path: (refernce ->) 10 -(intermediate)-> 9 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 9) 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 (10 -> 9) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !

{ The 1 th Path: (refernce ->) 9 -(intermediate)-> 10 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 10) has a NON-POSITIVE left-end shift (=0) and a NON-NEGATIVE right-end shift (=2): 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 (9 -> 10) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !


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

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

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

(ref_len, rec_len) = (3, 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 23 th segment ...


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


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


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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (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 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) = (24, 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} = 4) >>>>>


... 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) = (9, 8)

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

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

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

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

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

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

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

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

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

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

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

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


... 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) = (18, 18)

<<<<< 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 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) = (16, 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} = 5) >>>>>


... 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) = (17, 16)

<<<<< 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 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 : (0, 3) >

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 17 ,
#{columns in new reconstructed MSA} = 16 .

$baseline_shift_intm = 0 .

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

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

seq0000   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0001   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0002   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0003   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0004   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0005   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0006   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0007   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0008   	    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   -5   -5   -5    -    -    -    -    -    0
seq0013   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0014   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0015   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    0
seq0018   	  -16    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -    -    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

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





[WARNING 'classify_msa_errors_via_mblks.2val.pl'] Somehow, NO INDELS COULDN'T BE directly ASSOCIATED to the 2nd-moved c-block for the path: (0 -> 3) !

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 17 ,
#{columns in new reconstructed MSA} = 16 .

$baseline_shift_intm = 0 .

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

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

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

seq0000   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0007   	    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
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0018   	  -16    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (3 -> 0) ]

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

1st(intermediate)	0	2	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	None	26:16:16:-/26:0:15:X
2nd(reconstructed)	Merge(complementary)(+shift)(?)	3	26:0:15:X/26:16:16:-	26:1:15:X


{Total penalty} = 103 .





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

<<<<<< Segment ID: 31  (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 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) = (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 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) = (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 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) = (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} = 3) >>>>>


... 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 ... >>


< 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} = 9 ,
#{columns in new reconstructed MSA} = 9 .

$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

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



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

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

seq0000   	   -3   -3   -3   -3    -    -    -    -    -
seq0001   	   -3   -3   -3   -3    -    -    -    -    -
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
seq0006   	    0    0    0    0    -    -    -    0    0
seq0007   	    0    0    0    0    -    -    -    0    0
seq0008   	    0    0    0    0    -    -    -    0    0
seq0009   	    0    0    0    0    -    -    -    0    0
seq0013   	    0    0    0    0    -    -    -    0    0
seq0014   	    0    0    0    0    -    -    -    0    0
seq0015   	    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    -    -    -    0    0
seq0020   	    0    0    0    0    -    -    -    0    0





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

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

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


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

1st(intermediate)	Complex(???)	100	3:5:6:X	3:7:8:X/8:4:6:X
2nd(reconstructed)	Complex(???)	100	3:0:2:X/8:4:6:X	None


{Total penalty} = 200 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 9 ,
#{columns in new reconstructed MSA} = 9 .

$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

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



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

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

seq0000   	    0    0   -5   -5    -    -    -    -    -
seq0001   	    0    0   -5   -5    -    -    -    -    -
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
seq0006   	    0    0    0    0    -    -    -    0    0
seq0007   	    0    0    0    0    -    -    -    0    0
seq0008   	    0    0    0    0    -    -    -    0    0
seq0009   	    0    0    0    0    -    -    -    0    0
seq0013   	    0    0    0    0    -    -    -    0    0
seq0014   	    0    0    0    0    -    -    -    0    0
seq0015   	    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    -    -    -    0    0
seq0020   	    0    0    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: (0 -> 2) !


 --- Finished analysis for the segment 34 ! ---

<<<<<< Segment ID: 35  (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 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) = (74, 74)

<<<<< 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 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 ... >>


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 74 ,
#{columns in new reconstructed MSA} = 74 .

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

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    1    0    0
seq0008   	    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   -1   -1    -    0    0    0    0    0    -    1    0    0
seq0014   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0015   	   12  -13  -13  -13  -13  -13  -13  -13  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    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
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    -    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    1    1    1    1    1    -    2
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    0    0    0    -    -    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

seq0000   	    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
seq0002   	    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
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    0    0    0
seq0008   	    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
seq0014   	    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    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





[ 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	0	2	1	0	0


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

1st(intermediate)	Shift(???)	2	20:48:48:-	20:41:41:-
2nd(reconstructed)	Complex	100	21:50:50:X/20:41:41:-/22:42:42:-	20:41:42:-


{Total penalty} = 102 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 74 ,
#{columns in new reconstructed MSA} = 74 .

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

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    1    0    0
seq0008   	    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   -1   -1    -    0    0    0    0    0    -    1    0    0
seq0014   	    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0015   	   12  -13  -13  -13  -13  -13  -13  -13  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    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   -1   -1   -1    -    -    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1    -    -    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

seq0000   	    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
seq0002   	    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
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    0    0    0
seq0008   	    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
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    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





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

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

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


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

1st(intermediate)	Complex(???)	100	21:50:50:X	21:48:48:X/20:42:42:-
2nd(reconstructed)	Complex(???)	100	20:42:42:-/21:48:48:X	20:41:42:-


{Total penalty} = 200 .





< The 2 th pair : (4, 5) >

{ The 0 th Path: (refernce ->) 4 -(intermediate)-> 5 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 74 ,
#{columns in new reconstructed MSA} = 74 .

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

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    1    0    0
seq0008   	    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   -1   -1    -    0    0    0    0    0    -    1    0    0
seq0014   	    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0015   	   12    -    -    -    -    -    -    -    -    -    -    -    -    -    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    -    1    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    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
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    -    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    -    0
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    0    0    0    -    -    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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

seq0000   	    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
seq0002   	    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
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    0    0    0
seq0008   	    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
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0015   	    0  -13  -13  -13  -13  -13  -13  -13  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (4 -> 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	2	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	23:39:63:X/23:38:38:-	23:38:49:X/23:51:63:X
2nd(reconstructed)	Complex(???)	100	23:51:63:X/23:71:71:X	23:60:73:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 5 -(intermediate)-> 4 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 74 ,
#{columns in new reconstructed MSA} = 74 .

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

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    1    0    0
seq0008   	    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   -1   -1    -    0    0    0    0    0    -    1    0    0
seq0014   	    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0015   	    -  -13  -13  -13  -13  -13  -13  -13  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    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
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    -    -    0    0    0    0    0    0    0
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(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

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seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    -    0    0    0
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seq0015   	   12    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
seq0020   	    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 (5 -> 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	2	0	0	0	0
2nd(reconstructed)	1	1	0	0	0	0


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

1st(intermediate)	Complex(???)	100	23:39:63:X	23:39:50:X/23:60:73:X
2nd(reconstructed)	Shift	1	23:39:50:X	23:38:49:X


{Total penalty} = 101 .





 --- Finished analysis for the segment 36 ! ---



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

#{Segments skipped} = 0 .
#{Segments whose ComplLiMMent calculations skipped} = 0 .
#{Anomalous segments} = 0 .
#{Segments used as inputs} = 0 .
#{Segments successfully processed} = 36 .
#{Segments failed to be processed} = 0 .


real	0m2.363s
user	0m1.258s
sys	0m0.635s
