<<<<< 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 = 26 ,
#{Sites in the segment}_rec = 29 .


<< 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)     00000000001111111111222222
               01234567890123456789012345
                                         
seq0000        ACAAAT--GCTGCTTT------GATT
seq0001        ACAAAT--GCTGCTTT------GATT
seq0002        ACATAT--GCTGCTTT------GATT
seq0003        ACATAT--GCTGCTTT------GATT
seq0004        ACATAT--GCTGCTTT------GATT
seq0005        ACATAT--GCTGGTTT------GATT
seq0006        AGATAT--GCTGTTTT------GATT
seq0007        AGATAT--GCTGCTTT------GATT
seq0008        ACATATTTGCCTTGTT------GATT
seq0009        --ATAT--GCTTCGTT------GATT
seq0013        A-ATGT--GCATCGTT------GCTA
seq0014        ACATAT--CCTTCGTT---TGTAATG
seq0015        ATGTAT--GCTTCGTT------GATT
seq0018        ACGCTA--CCTT-GTTCAC---AATT
seq0020        ACATAA--CCTG-TTTCAC---GGTT


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222
               01234567890123456789012345678
                                            
seq0000        ACAAA--TGCTGCTTTG------ATT---
seq0001        ACAAA--TGCTGCTTTG------ATT---
seq0002        ACATA--TGCTGCTTTG------ATT---
seq0003        ACATA--TGCTGCTTTG------ATT---
seq0004        ACATA--TGCTGCTTTG------ATT---
seq0005        ACATA--TGCTGGTTTG------ATT---
seq0006        AGATA--TGCTGTTTTG------ATT---
seq0007        AGATA--TGCTGCTTTG------ATT---
seq0008        ACATATTTGCCTTGTTG------ATT---
seq0009        ----ATATGCTTCGTTG------ATT---
seq0013        A-ATG--TGCATCGTTG------CTA---
seq0014        ACATA--TCCTTCGTTT------GTAATG
seq0015        ATGTA--TGCTTCGTTG------ATT---
seq0018        AC------GCTACCTTGTTCACAATT---
seq0020        ACATA------ACCTGTTTCACGGTT---


<<<<< 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

seq0000   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0001   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0002   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0003   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0004   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0005   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0006   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0007   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0009   	    -    -    -    -    2    2    2    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0013   	    0    -    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0014   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -3    -    -    -    -    -    -    3    3    3    3    3    3
seq0015   	    0    0    0    0    0    -    -    2    0    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    -    -    -
seq0018   	    0    0    -    -    -    -    -    -    6    6    6    6    4    4    4    4    3    3    3    3    3    3    0    0    0    0    -    -    -
seq0020   	    0    0    0    0    0    -    -    -    -    -    -    6    4    4    4    4    3    3    3    3    3    3    0    0    0    0    -    -    -



<<<<< 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} = 8) >>

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

0	4	7	17	4	2	n/a	9
1	7	7	25	3	2	n/a	0,1,2,3,4,5,6,7,10,11,12
2	8	11	26	9	6	n/a	13
3	11	11	28	8	6	n/a	14
4	12	15	29	7	4	n/a	13,14
5	16	16	25	0	-6	n/a	0,1,2,3,4,5,6,7,8,9,10,12
6	16	28	21	1,6	-3,3	0	11
7	16	21	29	5	3	n/a	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} = 8) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 2): 1, 5 . ]


[ 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	4	4	Complex(???)	17:0:1:X/16:6:7:-	17:0:3:X
1	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
2	0	4	4	Complex	None	25:7:7:-/27:8:10:-
3	0	1	1	Complex(???)	None	27:8:10:-
4	0	4	4	Complex(???)	25:12:12:-	None
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	7	13	Shift(?)	21:19:21:-	21:26:28:-
7	0	6	6	Complex(???)	25:12:12:-/25:16:18:X	25:17:22:X


[ Contents of %indel_ref2assoc_cblks ]

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

17:0:1	0
20:1:1	{Equivalent to '20:1:1'(rec)}
16:6:7	0
25:12:12	4,7
25:16:18	7
21:19:21	6


[ Contents of %indel_rec2assoc_cblks ]

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

17:0:3	0
20:1:1	{Equivalent to '20:1:1'(ref)}
26:2:4	None
18:5:6	None
25:7:7	2
27:8:10	2,3
25:17:22	7
21:26:28	6


<<<< (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]

1	=> [0],
3	=> [2],


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

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

0	=> [1],
2	=> [3],


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

Indx_cblk_A	indx_cblk_B

4	7


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

[ For the 1 th pair: (4, 7) ]

