<<<<< Input Tree (Top_node = 29) >>>>>

( 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};


<<<<< Input MSA >>>>>

#{Sequences} = 15 .
#{Sites in the segment}_ref = 63 ,
#{Sites in the segment}_rec = 59 .


<< Correspondence between sequence IDs and sequence indices >>

Indx:	Seq_ID

0:	seq0000
1:	seq0001
2:	seq0002
3:	seq0003
4:	seq0004
5:	seq0005
6:	seq0006
7:	seq0007
8:	seq0008
9:	seq0009
10:	seq0013
11:	seq0014
12:	seq0015
13:	seq0018
14:	seq0020


<< Original Segment of the Reference Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GCAT-------------------------------------------------TGCCAGA
seq0001        G-----------------------------------------------------------
seq0002        GGAT-------------------------------------------------TGCCAGA
seq0003        GGAT-------------------------------------------------TGCCAGA
seq0004        GGAT-------------------------------------------------TGCCAGA
seq0005        CCAC----GATGCTA-GTACGGGTGCGGTACAC----ACG-------CAGTC-TGCCAGA
seq0006        CCAC----GATGCTA-GTACCGGTGCGGAA-AC----ACG-------CAGTC-TGCCAGA
seq0007        CCAC----GATGCT------CGGTCCGGAA-AC----GCG-------CAGTC-TGCCAGA
seq0008        CGTT----GATGCTA-GAACCGGTGCGTAG-TCGATCA----------TGTC-TGCCAGA
seq0009        CCAT----GATGCTA-GAACCGGTGCGTAG-TC----ACG-------CTGTC-TCCCAGA
seq0013        CCATCCCAGCTGCTT-GGACCGTAGGGTAG-AC----ACGCTTTACCCTACC-TGTCCGA
seq0014        CCATCCAAGATGCTA-GAACCAGAGCGCCG-TC----ACG-------CTGCC-TTCCAGA
seq0015        CCATCCAAAGTGCTATGAAGTGGTGCGTAG-TC----ATG-------CTGCC-TGACTGA
seq0018        TCATCCGAGATGCTA-GATCCGCTGCGTAG-AC----ATA-------CTGCC-TGTCAAA
seq0020        CCATCCAAGAGGC---GCATCGGTGCCTTG-CA----ACG-------CTACCTTGCCCAA

(position)     666
               012
                  
seq0000        GTG
seq0001        ---
seq0002        GCG
seq0003        GCG
seq0004        GCG
seq0005        GCG
seq0006        GCG
seq0007        GCG
seq0008        GCG
seq0009        GAG
seq0013        GGG
seq0014        TCG
seq0015        GCG
seq0018        GGG
seq0020        GTG


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333333334444444444555555555
               01234567890123456789012345678901234567890123456789012345678
                                                                          
seq0000        GCAT---------------------------------------------TGCCAGAGTG
seq0001        ----------------------------------------------------------G
seq0002        GGAT---------------------------------------------TGCCAGAGCG
seq0003        GGAT---------------------------------------------TGCCAGAGCG
seq0004        GGAT---------------------------------------------TGCCAGAGCG
seq0005        CCAC----GATGCTA-GTACGGGTGCGGTACAC-ACGCA-------GTCTGCCAGAGCG
seq0006        CCAC----GATGCTA-GTACCGGTGCGG-AAAC-ACGCA-------GTCTGCCAGAGCG
seq0007        CCAC----GATGCT------CGGTCCGG-AAAC-GCGCA-------GTCTGCCAGAGCG
seq0008        CGTT----GATGCTA-GAACCGGTGCGT-AGTCGATCAT-------GTCTGCCAGAGCG
seq0009        CCAT----GATGCTA-GAACCGGTGCGT-AGTC-ACGCT-------GTCTCCCAGAGAG
seq0013        CCATCCCAGCTGCTT-GGACCGTAGGGT-AGAC-ACGCTTTACCCTACCTGTCCGAGGG
seq0014        CCATCCAAGATGCTA-GAACCAGAGCGC-CGTC-ACGCT-------GCCTTCCAGATCG
seq0015        CCATCCAAAGTGCTATGAAGTGGTGCGT-AGTC-ATGCT-------GCCTGACTGAGCG
seq0018        TCATCCGAGATGCTA-GATCCGCTGCGT-AGAC-ATACT-------GCCTGTCAAAGGG
seq0020        CCATCCAAGAGGC---GCATCGGTGCCT-TGCA-ACGCT------ACCTTGCCCAAGTG


<<<<< 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... >>>>>

<< Output of 'map_shifts_respos_bw_2msas' >>

($shift_lf, $shift_rf) = (0, -4) .

[ Shifts in the Reconstructed MSA ]

(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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4
seq0003   	    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4
seq0004   	    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4
seq0005   	    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
seq0006   	    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
seq0007   	    0    0    0    0    -    -    -    -    0    0    0    0    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -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    -    1    1    0    0    0    0    0    0    0  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
seq0009   	    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
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    -    1    1    0    0    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -4
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    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
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    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
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    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -    -   -3   -3   -3   -4
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    -    1    1    0    0    -   -3   -3   -3  -10  -10    -    -    -    -    -    -   -4   -4   -4   -4   -4



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

seq0000   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0001   	    -    -    -    -    -    -    -    -   58
seq0002   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0003   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0004   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0005   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0006   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0007   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0008   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0009   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0013   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0014   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0015   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0018   	   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0020   	   -4   -4   -4   -4   -4   -4   -4   -4   -4



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

<< Output of 'br_list_classes_shift_respos' >>

$commoner_shift_flank = 0 .


<<<<< 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... >>>>>

... NO CHANGES were made ...


<<<<< 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. >>>>>

<< Output of 'lump_together_similar_blocks': Content of @{$composite_miniblocks} (#{composite_miniblocks} = 9) >>

Indx_cmp_miniblock	beg_cmb	end_cmb	mrca	indices,constituent,miniblocks	list,position,shifts	merger,types	indices,involved,seqs

0	29	30	29	9	1	n/a	6,7,8,9,10,11,12,13,14
1	34	48	20	6	-3	n/a	10
2	34	36	29	4	-3	n/a	5,6,7,9,11,12,13,14
3	37	38	29	0	-10	n/a	5,6,7,9,11,12,13,14
4	38	38	16	1	-10	n/a	8
5	45	58	28	3	-4	n/a	14
6	46	48	27	5	-3	n/a	5,6,7,8,9,11,12,13
7	49	58	27	2	-4	n/a	0,2,3,4,5,6,7,8,9,10,11,12,13
8	58	58	2	10	58	n/a	1



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

<<< (1) For Reference MSA >>>

<<< (2) For Reconstructed MSA >>>

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

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 9) >>>>>


[[ Results of the Main Process (1st Round) ]]

[ Contents of @cblk_wise_cts_invlvd_indels ]

Indx_cmp_blk	#{rlv_indels}_ref	#{rlv_indels}_rec	#{rltd_indels}_ref	#{rltd_indels}_rec	#{other_involved}_ref	#{other_involved}_rec

0	1	1	0	0	0	0
1	1	1	0	0	0	0
2	2	1	0	0	0	0
3
4	1	0	0	0	0	0
5	1	0	0	1	0	0
6
7
8	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 3, 6, 7 . ]


[ Contents of @cblk_wise_msa_errors ]

Indx_cmp_blk	Indx_error	len_cblk_ref	len_cblk_rec	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(ref)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(rec)

0	0	2	2	Shift	10:30:30:-	10:28:28:-
1	0	15	15	Complex(???)	20:40:46:-	20:39:44:-
2	0	3	3	Merge(complementary)	16:33:36:-/16:38:47:X	16:33:33:-
3	Skipped!!(NO_RELEVANT_BRANCH)
4	0	1	1	Complex(???)	16:38:47:X	None
5	0	14	14	Complex(???)	28:52:52:-	26:45:45:X
6	Skipped!!(NO_RELEVANT_BRANCH)
7	Skipped!!(NO_RELEVANT_BRANCH)
8	0	1	1	Shift	2:1:62:X	2:0:57:X


[ Contents of %indel_ref2assoc_cblks ]

Br:beg:end(ref)	indices,of,associated,composite-blocks

2:1:62	8
19:4:7	{Equivalent to '19:4:7'(rec)}
9:8:51	{Equivalent to '9:8:48'(rec)}
27:13:14	None
12:14:19	{Equivalent to '12:14:19'(rec)}
23:15:15	{Equivalent to '23:15:15'(rec)}
10:30:30	0
16:33:36	2
16:38:47	2,4
20:40:46	1
28:52:52	5


[ Contents of %indel_rec2assoc_cblks ]

Br:beg:end(rec)	indices,of,associated,composite-blocks

2:0:57	8
19:4:7	{Equivalent to '19:4:7'(ref)}
9:8:48	{Equivalent to '9:8:51'(ref)}
27:13:14	None
12:14:19	{Equivalent to '12:14:19'(ref)}
23:15:15	{Equivalent to '23:15:15'(ref)}
10:28:28	0
16:33:33	2
20:39:44	1
26:45:45	5
23:45:45	None
21:45:45	None
19:45:45	None


<<<< (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... >>>>

[[ Interim Results ]]

[ Contents of %cb2hard_linked (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linked,by,the,key]

6	=> [1],
7	=> [5],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linking,the,key]

1	=> [6],
5	=> [7],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 1) ]

Indx_cblk_A	indx_cblk_B

2	4


[[ Results of the Main Process (2nd Round) ]]

[ For the 1 th pair: (2, 4) ]

