<<<<< 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 = 51 ,
#{Sites in the segment}_rec = 48 .


<< 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)     000000000011111111112222222222333333333344444444445
               012345678901234567890123456789012345678901234567890
                                                                  
seq0000        AGCG-GG-AACTGC---ATA-ACAACC-------------GTATG-GGT--
seq0001        AGCG-GG-AACTGC---ATA-ACAACC-------------GTATG-GGT--
seq0002        AGCG-GG-AACTGC---ATA-ACAACC-------------GTAAG-GGT--
seq0003        AGCG-GG-AACTGC---ATA-ACAACC-------------GTATG-CGT--
seq0004        AGCG-GG-AACTGC---ATA-ACAACC-------------GTATG-GGT--
seq0005        -------------------------------------------TG-GCT--
seq0006        -------------------------------------------TG-GGT--
seq0007        -------------------------------------------TG-GGT--
seq0008        ATCG-GGTTTCTTT---AGT-ACAAGCTTGGGGACCCCACGTAAG-GGT--
seq0009        ATCG-AG-TACTTT---AGT-TCAAGATTGGGGTCCGCACCGTTG-AGTTG
seq0013        AGCCGTC-AATTGC---AGAGACTAGC-------------GTTACCCGT--
seq0014        AGCC-GG-TCTTTC---CGAGAGAAGC-------------GCGTC-GGT--
seq0015        AGCC-GG-AATTTC---AGAGACAAGC-------------GAGTA-GTT--
seq0018        AACG-TA-AATTTCCGCAGA-ACTACC-------------GTGTT-GGG--
seq0020        AGCG-AG-AACTCCCGCTGA-ACAAGC-------------TTGTA-TCG--


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        AGCGGG-AACTGCATA---ACAAC--------------CG-TATGGGT
seq0001        AGCGGG-AACTGCATA---ACAAC--------------CG-TATGGGT
seq0002        AGCGGG-AACTGCATA---ACAAC--------------CG-TAAGGGT
seq0003        AGCGGG-AACTGCATA---ACAAC--------------CG-TATGCGT
seq0004        AGCGGG-AACTGCATA---ACAAC--------------CG-TATGGGT
seq0005        -------------------------------------------TGGCT
seq0006        -------------------------------------------TGGGT
seq0007        -------------------------------------------TGGGT
seq0008        ATCGGGTTTCTTTAGT---ACAAGCTTGGGGACCCC-ACG-TAAGGGT
seq0009        ATCGAG-TACTTTAGT---TCAAGATTGGGGTCCGCACCGTTGAGTTG
seq0013        AGCCGTCAATTGCAGA--GACTAG--------------CGTTACCCGT
seq0014        AGCCGG-TCTTTCCGA--GAGAAG--------------CG-CGTCGGT
seq0015        AGCCGG-AATTTCAGA--GACAAG--------------CG-AGTAGTT
seq0018        AACGTA-AATTTCCGCAGAACTAC--------------CG-TGTTGGG
seq0020        AGCGAG-AACTCCCGCTGAACAAG--------------CT-TGTATCG


<<<<< 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, -3) .

[ 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

seq0000   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0001   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0002   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0003   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0004   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0   -1   -1   -1
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0   -1   -1   -1
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0   -1   -1   -1
seq0008   	    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -1    -    0    0    0    0   -1   -1   -1
seq0009   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3
seq0013   	    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0015   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0018   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1
seq0020   	    0    0    0    0   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -   12   -1    -    0    0    0    0   -1   -1   -1



<<<<< 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} = 12) >>

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

0	4	12	25	9	-1	n/a	0,1,2,3,4,8,9,11,12
1	4	18	29	8	-1	n/a	13,14
2	7	12	20	11	-1	n/a	10
3	13	15	25	0	-4	n/a	0,1,2,3,4,8,9,10,11,12
4	18	23	24	3	-2	n/a	10,11,12
5	19	23	29	2	-2	n/a	0,1,2,3,4,13,14
6	19	39	16	4,10	-2,-1	0	8
7	19	47	17	5,1	-2,-3	0	9
8	38	38	29	14	12	n/a	0,1,2,3,4,10,11,12,13,14
9	39	39	29	6	-1	n/a	0,1,2,3,4,11,12,13,14
10	39	47	20	12	-1	n/a	10
11	45	47	29	7	-1	n/a	0,1,2,3,4,5,6,7,8,11,12,13,14



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


[[ 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	0	0	0	0	0	0
1	1	2	1	1	0	0
2	0	0	0	1	0	0
3	0	0	0	0	0	0
4	1	0	0	2	0	0
5
6	0	1	0	0	0	0
7	1	1	0	0	0	0
8
9
10	1	0	0	0	0	0
11


[ Skipped Composite-Blocks (#{cblocks} = 6): 0, 3, 5, 8, 9, 11 . ]


[ 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	Skipped!!(NO_ASSOCIATED_EVENT(???))
1	0	15	15	Complex	25:14:16:X/24:20:20:-	25:6:6:-/25:16:17:X/19:18:18:X
2	0	6	6	NO_ASSOCIATED_EVENT(???)	None	21:6:6:X
3	Skipped!!(NO_ASSOCIATED_EVENT(???))
4	0	6	6	Complex	24:20:20:-	25:16:17:X/19:18:18:X
5	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
6	0	20	21	Complex(???)	None	16:40:40:X
7	0	30	29	Complex(???)	17:49:50:-	17:36:36:-
8	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
9	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
10	0	9	9	Complex(???)	20:45:45:-	None
11	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

14:0:42	None
20:4:4	None
16:7:7	None
25:14:16	1
24:20:20	1,4
18:27:39	None
20:45:45	10
17:49:50	7


[ Contents of %indel_rec2assoc_cblks ]

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

14:0:42	None
25:6:6	1
23:6:6	None
21:6:6	2
17:6:6	None
15:6:6	None
25:16:17	1,4
19:18:18	1,4
18:24:37	None
17:36:36	7
25:40:40	None
23:40:40	None
21:40:40	None
16:40:40	6
15:40:40	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} = 4) ]

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

0	=> [1],
5	=> [4,6,7],
9	=> [6,10],
11	=> [10],


[ Contents of %cb2hard_linking (#{keys} = 5) ]

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

1	=> [0],
4	=> [5],
6	=> [5,9],
7	=> [5],
10	=> [9,11],


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

Indx_cblk_A	indx_cblk_B

1	4


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

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

