[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_0000004 .

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_inp0000004.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.0000004.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_inp0000004.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.0000004.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.0000004.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.0000004.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} = 36

Seg_ID	Start_in_Ref	End_in_ref	Start_in_Rec	End_in_Rec	Diagnosis

0	0	81	0	100	CLEARLY_DIFFERENT
1	95	287	114	304	CLEARLY_DIFFERENT
2	305	314	322	331	CLEARLY_DIFFERENT
3	316	495	333	509	CLEARLY_DIFFERENT
4	498	531	512	545	CLEARLY_DIFFERENT
5	536	561	550	575	CLEARLY_DIFFERENT
6	566	570	580	583	CLEARLY_DIFFERENT
7	579	589	592	602	CLEARLY_DIFFERENT
8	598	602	611	615	CLEARLY_DIFFERENT
9	614	616	627	629	CLEARLY_DIFFERENT
10	619	626	632	639	CLEARLY_DIFFERENT
11	631	881	644	847	CLEARLY_DIFFERENT
12	885	999	851	932	CLEARLY_DIFFERENT
13	1008	1010	941	943	CLEARLY_DIFFERENT
14	1012	1041	945	978	CLEARLY_DIFFERENT
15	1091	1206	1028	1143	CLEARLY_DIFFERENT
16	1207	1209	1144	1146	CLEARLY_DIFFERENT
17	1213	1238	1150	1175	CLEARLY_DIFFERENT
18	1242	1247	1179	1184	CLEARLY_DIFFERENT
19	1265	1276	1202	1213	CLEARLY_DIFFERENT
20	1282	1289	1219	1226	CLEARLY_DIFFERENT
21	1318	1322	1255	1259	CLEARLY_DIFFERENT
22	1328	1330	1265	1267	CLEARLY_DIFFERENT
23	1333	1336	1270	1273	CLEARLY_DIFFERENT
24	1369	1403	1306	1335	CLEARLY_DIFFERENT
25	1460	1471	1392	1402	CLEARLY_DIFFERENT
26	1494	1500	1425	1431	CLEARLY_DIFFERENT
27	1517	1532	1448	1463	CLEARLY_DIFFERENT
28	1544	1547	1475	1477	CLEARLY_DIFFERENT
29	1548	1601	1478	1516	CLEARLY_DIFFERENT
30	1603	1614	1518	1528	CLEARLY_DIFFERENT
31	1615	1619	1529	1532	CLEARLY_DIFFERENT
32	1624	1667	1537	1582	CLEARLY_DIFFERENT
33	1669	1673	1584	1588	CLEARLY_DIFFERENT
34	1678	1692	1593	1607	CLEARLY_DIFFERENT
35	1693	1695	1608	1610	CLEARLY_DIFFERENT



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

#{sequences in MSA} =  15 .
#{columns in MSA}   = 1695 .


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

#{columns in MSA} = 1610 .


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

#{columns in MSA} = 1695 .


<<<<< 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) = (81, 100)

<<<<< 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} = 20) >>>>>


... 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 ... >>


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

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

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

(ref_len, rec_len) = (192, 190)

<<<<< 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 160, 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 1 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


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

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

(ref_len, rec_len) = (9, 9)

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

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

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

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

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

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

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

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

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

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

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

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


... The MAIN PROCESS (1st Round) ENDED for the 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) = (179, 176)

<<<<< 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 2 gaps longer than 120. So, I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 3 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


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

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

(ref_len, rec_len) = (33, 33)

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

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (4, 3)

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (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 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) = (4, 4)

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

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

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

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

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

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

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

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

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

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

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

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


... The MAIN PROCESS (1st Round) ENDED for the 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) = (7, 7)

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

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

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

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

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

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

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

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

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

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

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

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


... The MAIN PROCESS (1st Round) ENDED for the 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) = (250, 203)

<<<<< 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} = 45) >>>>>


... 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 ... >>


< The 1 th pair : (10, 13) >

{ The 0 th Path: (refernce ->) 10 -(intermediate)-> 13 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (10 -> 13) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !

{ The 1 th Path: (refernce ->) 13 -(intermediate)-> 10 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (13 -> 10) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !


< The 2 th pair : (24, 25) >

{ The 0 th Path: (refernce ->) 24 -(intermediate)-> 25 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 250 ,
#{columns in new reconstructed MSA} = 250 .

$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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47   47
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47    -    -



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

seq0000   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0001   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0002   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0003   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0004   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0005   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0006   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0007   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0008   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0009   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0013   	   47   47   17   17   17   17   16   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -   -5   -5   -5    -    -    -    -    -    -    -    -    -    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0014   	    -    -    -    -    -    -    -    -    -   58   58   58   58   58   58   58   58    -   59   59   59    -    -    -    -    -    -    -    -    -   68   68   68   68   68   68   68   68   68   68   68   68    -   69    -   70   70   70   70   70
seq0015   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28   28   28    -    -    -    -    -    -    -    -    -   37   37   37   37   37   37   37    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0020   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

seq0000   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0001   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0002   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0003   	    4    -    -    6    6    -    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0004   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0005   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0006   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0007   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0008   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   40   40
seq0009   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0013   	    4    4    4    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0
seq0014   	   70   70   70   70   70   70   70   70   70    -   70   48    -    -   50   50   50   50   50   50   50   50   46   46   46   46   46   46   46   46   46   46   46   46   46   46   46   45   45   45   45   45   45   45   45    -    -   47   47   47
seq0015   	   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   48   48    -    -    -   51   51   51   51   51   51   51   51   51   51   51   50   49   25   25   25   25   25   25   25   25
seq0018   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0020   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195  196  197  198  199

seq0000   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0001   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0002   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0003   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0004   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0005   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0006   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0007   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0008   	   40   -5   -5    -    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0009   	   25   25   25   25   -1   -1    -    -    -    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    2    1    1    1    1    1    1    1    1
seq0013   	    0    0    0    0    -    0    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0014   	   47   47   47   47   47   47   47    -    -   49   49   49   49   49   49   49   49    -    -    -   52   52   52   52   52    -   53   53   53   53   53   53   27    -    -   29   29   29   29   29   29   29   29   29   29   29   29   29   29    -
seq0015   	   25   25   25   25    -    0    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0018   	   25   25   25   25    -    0    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -
seq0020   	   25   25   25   25    -    0    0    0    -    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -



(position)	  200  201  202  203  204  205  206  207  208  209  210  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225  226  227  228  229  230  231  232  233  234  235  236  237  238  239  240  241  242  243  244  245  246  247  248  249

seq0000   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    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   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0009   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0013   	    1    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   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -   36   36   36   36   35   35   34   34   34    -   35   35   35   35   35   35   35   35   35    -   36   36   36   36   36   36   36   36    -    -    -    -    -    -    -   43   43    -    -    -    -    -    -    -
seq0015   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    -    -    0    0    0    0    0    0
seq0018   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0



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

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    -    -



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

seq0000   	    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    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
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
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
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
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
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
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
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    0    -    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

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
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
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
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
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
seq0005   	    0    -    -    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0006   	    0    -    -    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
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
seq0008   	    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
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    -    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    -    -    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
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



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195  196  197  198  199

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



(position)	  200  201  202  203  204  205  206  207  208  209  210  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225  226  227  228  229  230  231  232  233  234  235  236  237  238  239  240  241  242  243  244  245  246  247  248  249

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
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
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
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
seq0006   	    0    0    0    0    0    -    0    0    0    -    -    -    -    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    -    0    0    0    -    -    -    -    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
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
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
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
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    -    -    -    -    -    -    -
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (24 -> 25) ]

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

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


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

1st(intermediate)	Complex	100	19:204:205:X	15:158:158:-/19:156:156:X/19:205:205:X/18:157:157:X
2nd(reconstructed)	Complex	100	19:156:156:X/25:154:154:-/15:158:158:-/18:157:157:X	19:156:156:X/15:157:158:-


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 25 -(intermediate)-> 24 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 24) has a NON-POSITIVE left-end shift (=0) and a NON-NEGATIVE right-end shift (=1): 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 (25 -> 24) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !


< The 3 th pair : (35, 36) >

{ The 0 th Path: (refernce ->) 35 -(intermediate)-> 36 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (35 -> 36) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 36 -(intermediate)-> 35 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (36 -> 35) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !


< The 4 th pair : (39, 42) >

{ The 0 th Path: (refernce ->) 39 -(intermediate)-> 42 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (39 -> 42) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 42 -(intermediate)-> 39 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (42 -> 39) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !


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

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

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

(ref_len, rec_len) = (114, 81)

<<<<< 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} = 14) >>>>>


... 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 ... >>


< The 1 th pair : (13, 10) >

{ The 0 th Path: (refernce ->) 13 -(intermediate)-> 10 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 81 ,
#{columns in new reconstructed MSA} = 81 .

$baseline_shift_intm = 0 .

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

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

seq0000   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    4    4    4    4    4    4    4    4    4
seq0014   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -  -30  -30  -31  -31  -31    -    -    -    -    -
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  -34  -34  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35    -
seq0018   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80

seq0000   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0001   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0002   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0003   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0004   	    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0005   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0006   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0007   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0008   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -    -    0    -  -33  -33
seq0009   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -    -    0    -    1    1
seq0013   	    4    4    4    4    4    4    4    4    4    -    5    5    5    5    5    5    5    5    5    5    5    -    -    -    8    8    8    8   -1  -33  -33
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1  -33  -33
seq0015   	  -34  -34  -34  -34  -34  -34  -34  -34  -34    -  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33
seq0018   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0020   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33



[[ 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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    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    0    0    0    0    0    0    0    0    0    0    0    -
seq0018   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80

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    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    -    -    -    -    -    -    -    -    -    -    -   -1    -    -    0    0
seq0009   	    -    -    -    -    -    -    -    -    0    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -   -1    -    -    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    -    0    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
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 (13 -> 10) ]

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

1st(intermediate)	1	0	1	1	0	0
2nd(reconstructed)	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	17:112:113:X/16:78:79:X	18:78:78:X
2nd(reconstructed)	Merge(same-type)	2	18:76:76:X/18:78:78:X	18:77:78:X


{Total penalty} = 102 .




{ The 1 th Path: (refernce ->) 10 -(intermediate)-> 13 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 81 ,
#{columns in new reconstructed MSA} = 81 .

$baseline_shift_intm = 0 .

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

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

seq0000   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    4    4    4    4    4    4    4    4    4
seq0014   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -  -30  -30  -31  -31  -31    -    -    -    -    -
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  -34  -34  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35    -
seq0018   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80

seq0000   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0001   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0002   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0003   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0004   	    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0005   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0006   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0007   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0008   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1    -    -  -33  -33
seq0009   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1    -    0    0    -
seq0013   	    4    4    4    4    4    4    4    4    4    -    5    5    5    5    5    5    5    5    5    5    5    -    -    -    8    8    8    8   -1  -33  -33
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1  -33  -33
seq0015   	  -34  -34  -34  -34  -34  -34  -34  -34  -34    -  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33
seq0018   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0020   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33



[[ 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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    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    0    0    0    0    0    0    0    0    0    0    0    -
seq0018   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80

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    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
seq0009   	    -    -    -    -    -    -    -    -    0    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    1    1
seq0013   	    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    -    0    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
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 (10 -> 13) ]

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

1st(intermediate)	0	1	1	0	0	0
2nd(reconstructed)	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)	Complex(???)	100	16:78:79:X	18:77:77:X
2nd(reconstructed)	Complex	100	17:80:80:X/18:77:77:X/16:78:78:X	18:77:78:X


{Total penalty} = 200 .





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

<<<<<< Segment ID: 13  (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 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) = (29, 33)

<<<<< 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 14 th segment ...


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


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


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

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

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

(ref_len, rec_len) = (115, 115)

<<<<< 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 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 ... >>


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 115 ,
#{columns in new reconstructed MSA} = 115 .

$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    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    -    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



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

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



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114

seq0000   	    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
seq0002   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    0    0    0    0    0    0    -    1    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



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

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

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



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

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



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114

seq0000   	    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
seq0002   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    0    0    0    0    0    0    -    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   82
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   82
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   82
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   82
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   82





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 5) ]

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

1st(intermediate)	1	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	19:8:114:-	19:2:26:-/19:33:114:-
2nd(reconstructed)	Shift	1	19:33:114:-	19:32:113:-


{Total penalty} = 3 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 115 ,
#{columns in new reconstructed MSA} = 115 .

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



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

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



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114

seq0000   	    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
seq0002   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    0    0    0    0    0    0    -    1    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107



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

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

seq0000   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



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

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



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114

seq0000   	    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
seq0002   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    0    0    0    0    0    0    -    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    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 (5 -> 1) ]

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

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


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

1st(intermediate)	Shift	1	19:8:114:-	19:7:113:-
2nd(reconstructed)	Complex	100	19:7:113:-/19:2:2:-/18:1:1:X	19:2:26:-/19:32:113:-


{Total penalty} = 101 .





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

<<<<<< Segment ID: 16  (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 16 th segment ...


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


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


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

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

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

(ref_len, rec_len) = (25, 25)

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

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

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

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

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

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

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

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

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

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

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

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


... 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) = (5, 5)

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (11, 11)

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (4, 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 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) = (2, 2)

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

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

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

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

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

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

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

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

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

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

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

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


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


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


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


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

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

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

(ref_len, rec_len) = (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 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) = (34, 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} = 12) >>>>>


... 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) = (11, 10)

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

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

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

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

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

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

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

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

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

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

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

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


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


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 11 ,
#{columns in new reconstructed MSA} = 10 .

$baseline_shift_intm = 0 .

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

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

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

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


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

1st(intermediate)	Shift	1	26:1:2:X	26:5:7:X
2nd(reconstructed)	Merge(complementary)	2	26:5:7:X/26:10:10:-	26:5:5:X


{Total penalty} = 3 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

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

$baseline_shift_intm = 0 .

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

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

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

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





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

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

1st(intermediate)	1	0	0	1	0	5
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)	Collapse-of-Independent-Insertions(+shift)(+4)(?)	11	11:6:6:-/26:9:9:-	27:6:6:-/24:6:9:X/18:6:6:X/9:6:6:X/10:6:6:X/12:6:6:X
2nd(reconstructed)	Inter-branch-transfer(ref>rec)(??)	7	26:1:2:X/27:6:6:-	26:5:5:X


{Total penalty} = 18 .





 --- Finished analysis for the segment 25 ! ---

<<<<<< Segment ID: 26  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (6, 6)

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

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

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

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

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

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

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

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

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

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

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

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


... The MAIN PROCESS (1st Round) ENDED for the 26 th segment ...


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


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


 --- Finished analysis for the segment 26 ! ---

<<<<<< Segment ID: 27  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (15, 15)

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

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

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

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

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

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

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

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

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

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

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

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 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) = (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 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) = (53, 38)

<<<<< 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} = 13) >>>>>


... 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 ... >>


< The 1 th pair : (5, 2) >

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


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (5 -> 2) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

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


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


< The 2 th pair : (9, 7) >

{ The 0 th Path: (refernce ->) 9 -(intermediate)-> 7 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (9 -> 7) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !

{ The 1 th Path: (refernce ->) 7 -(intermediate)-> 9 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (7 -> 9) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


< The 3 th pair : (10, 12) >

{ The 0 th Path: (refernce ->) 10 -(intermediate)-> 12 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 42 ,
#{columns in new reconstructed MSA} = 38 .

$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

seq0000   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0001   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0002   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0003   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0004   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0005   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -    -    -    -    -    0    0
seq0006   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -    -    -    -    -    0    0
seq0007   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -    -    -    -    -    0    0
seq0008   	    0    -    1    1    1    1    1   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0009   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0014   	    0    -    1    1    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0015   	    0    0    0    0    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0018   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4    -    -    -    -
seq0020   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15    -    -    -    -



[[ 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

seq0000   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0001   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0002   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0003   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0004   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0005   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -   -4   -4
seq0006   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -   -4   -4
seq0007   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -   -4   -4
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
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
seq0013   	    -    -    -    -    -    -    -    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
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
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (10 -> 12) ]

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

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


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

1st(intermediate)	Complex(???)	100	14:21:38:X	14:34:37:X
2nd(reconstructed)	Complex(???)	100	14:40:41:-	14:34:35:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 12 -(intermediate)-> 10 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 38 ,
#{columns in new reconstructed MSA} = 38 .

$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

seq0000   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0001   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0002   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0003   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0004   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0005   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -    -    -   -4   -4   -4
seq0006   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -    -    -   -4   -4   -4
seq0007   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -    -    -   -4   -4   -4
seq0008   	    0    -    1    1    1    1    1   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -   -4   -4   -4   -4
seq0009   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0013   	    -    -    -    -    -    -    -    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0014   	    0    -    1    1    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0015   	    0    0    0    0    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0018   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0020   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15



[[ 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

seq0000   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0001   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0002   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0003   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0004   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    0    0    0    0
seq0005   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0
seq0006   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0
seq0007   	    0    -    0    0    0    0    0    0    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    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
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
seq0013   	    -    -    -    -    -    -    -    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
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
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
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





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (12 -> 10) ]

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

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


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

1st(intermediate)	Shift(???)	2	14:21:38:X	14:29:34:X
2nd(reconstructed)	Shift	1	14:29:34:X	14:34:35:X


{Total penalty} = 3 .





< The 4 th pair : (10, 8) >

{ The 0 th Path: (refernce ->) 10 -(intermediate)-> 8 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (10 -> 8) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !

{ The 1 th Path: (refernce ->) 8 -(intermediate)-> 10 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (8 -> 10) canNOT be undone completely because of the failure type, $if_success = -13: No such file or directory !


 --- Finished analysis for the segment 29 ! ---

<<<<<< Segment ID: 30  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (11, 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} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 30 th segment ...


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


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


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

<<<<<< Segment ID: 31  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (4, 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) = (43, 45)

<<<<< 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 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 ... >>


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

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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 45 ,
#{columns in new reconstructed MSA} = 45 .

$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

seq0000   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0001   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0002   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0003   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0004   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0005   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0006   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0007   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0008   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    -    -    5    5    5    5    5    5    5    5    -    -    7    7    7    7    6    6
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    -    -    2    2    2    2    2    2
seq0013   	    0    0    0    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0014   	    0    0    0    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0015   	  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2
seq0020   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2



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

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

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
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
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
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
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
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
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
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
seq0008   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    0    0    -    -    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
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
seq0015   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2
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
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





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

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

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


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

1st(intermediate)	Complex(???)	100	23:0:29:X/23:32:37:X	23:2:37:X
2nd(reconstructed)	Merge(same-type)	2	23:2:37:X/23:43:44:X	23:2:39:X


{Total penalty} = 102 .




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

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 45 ,
#{columns in new reconstructed MSA} = 45 .

$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

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



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

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

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
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
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
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
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
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
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
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
seq0008   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    0    0    -    -    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0013   	    0    0    0    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -    -    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
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
seq0015   	  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
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





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

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

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


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

1st(intermediate)	Complex(???)	100	23:32:37:X	23:32:39:X
2nd(reconstructed)	Merge(same-type)	2	23:0:29:X/23:32:39:X	23:2:39:X


{Total penalty} = 102 .





 --- Finished analysis for the segment 32 ! ---

<<<<<< Segment ID: 33  (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 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) = (14, 14)

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

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

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

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

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

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

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

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

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

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

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

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


... The MAIN PROCESS (1st Round) ENDED for the 34 th segment ...


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


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


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

<<<<<< Segment ID: 35  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

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

(ref_len, rec_len) = (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 ! ---



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

#{Segments skipped} = 0 .
#{Segments whose ComplLiMMent calculations skipped} = 0 .
#{Anomalous segments} = 0 .
#{Segments used as inputs} = 0 .
#{Segments successfully processed} = 34 .
#{Segments failed to be processed} = 0 .


real	0m2.220s
user	0m1.229s
sys	0m0.566s
