<<<<< 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 = 48 ,
#{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)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0001        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0002        -ATAC--------CTCTAGTGCACCTCCGCACCGAAC---CAAT-TAA
seq0003        -ATAT--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAA
seq0004        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAA
seq0005        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAA-TAT
seq0006        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0007        -ATAC--------CTCTAGAGCACCTCCGCACCGAAC---CAGT-TAT
seq0008        -CTCC------ACCCCGAACGCACCTCCGAACCGCAC------T-TGT
seq0009        -GTAC------ACCACCAGCGCATCTGCGTTCTGAAC------T-TGG
seq0013        -ATAC------AC-----------------------------------
seq0014        -ATAG------ACCTCGAGGGCACCTCCGCCCCGTAA------T-TAT
seq0015        AAATC------GCCTCGAGGGCACCTCGGCACCGAACGGT---TATAT
seq0018        -ATACGTTGTGACCTGGAGGGCAGTTACCTACCGAAC------T-TAT
seq0020        -GTAC------ACCTAGAGGGCATCTCCGCACCGAAG------T-TAT


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        AT---------ACCTCTAGGGCACCTCCGCACCGAA----CCAATTAT
seq0001        AT---------ACCTCTAGGGCACCTCCGCACCGAA----CCAATTAT
seq0002        AT---------ACCTCTAGTGCACCTCCGCACCGAA----CCAATTAA
seq0003        AT---------ATCTCTAGGGCACCTCCGCACCGAA----CCAATTAA
seq0004        AT---------ACCTCTAGGGCACCTCCGCACCGAA----CCAATTAA
seq0005        AT---------ACCTCTAGGGCACCTCCGCACCGAA----CCAAATAT
seq0006        AT---------ACCTCTAGGGCACCTCCGCACCGAA----CCAATTAT
seq0007        AT---------ACCTCTAGAGCACCTCCGCACCGAA----CCAGTTAT
seq0008        CTC-C------ACCCCGAACGCACCTCCGAACCGCA----C---TTGT
seq0009        GTA-C------ACCACCAGCGCATCTGCGTTCTGAA----C---TTGG
seq0013        ATA-C------AC-----------------------------------
seq0014        ATA-G------ACCTCGAGGGCACCTCCGCCCCGTA----A---TTAT
seq0015        AAATC------GCCTCGAGGGCACCTCGGCACCGAACGGTT---ATAT
seq0018        ATA-CGTTGTGACCTGGAGGGCAGTTACCTACCGAA----C---TTAT
seq0020        GTA-C------ACCTAGAGGGCATCTCCGCACCGAA----G---TTAT


<<<<< 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, 0) .

[ 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   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0001   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0002   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0003   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0004   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0005   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0006   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0007   	   -1   -1    -    -    -    -    -    -    -    -    -    8    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    1    1    1    1    0    0    0
seq0008   	   -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    -    -    -    -    4    -    -    -    1    0    0    0
seq0009   	   -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    -    -    -    -    4    -    -    -    1    0    0    0
seq0013   	   -1   -1   -1    -    0    -    -    -    -    -    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	   -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    -    -    -    -    4    -    -    -    1    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   -3    -    -    -    0    0    0    0
seq0018   	   -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    -    -    -    -    4    -    -    -    1    0    0    0
seq0020   	   -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    -    -    -    -    4    -    -    -    1    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} = 7) >>

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

0	0	1	15	2	-1	n/a	0,1,2,3,4,5,6,7
1	0	2	29	1	-1	n/a	8,9,10,11,13,14
2	11	12	15	8	8	n/a	0,1,2,3,4,5,6,7
3	40	40	29	7	4	n/a	0,1,2,3,4,5,6,7,8,9,11,13,14
4	40	40	23	0	-3	n/a	12
5	41	44	15	6	1	n/a	0,1,2,3,4,5,6,7
6	44	44	29	5	1	n/a	8,9,11,13,14



<<<<< 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} = 7) >>>>>


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


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


[ 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	Complex(???)	None	15:2:4:X
1	0	3	3	Shift	23:0:0:-	23:3:3:-
2	0	2	2	Shift	15:11:12:X	15:2:4:X
3	Skipped!!(NO_RELEVANT_BRANCH)
4	0	1	1	Merge(same-type)	23:37:39:-/23:44:44:-	23:36:39:-
5	Skipped!!(NO_ASSOCIATED_EVENT(???))
6	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:0	1
26:5:10	{Equivalent to '26:5:10'(rec)}
15:11:12	2
20:13:47	{Equivalent to '20:13:47'(rec)}
23:37:39	4
15:40:42	{Equivalent to '15:41:43'(rec)}
23:44:44	4


[ Contents of %indel_rec2assoc_cblks ]

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

15:2:4	0,2
23:3:3	1
26:5:10	{Equivalent to '26:5:10'(ref)}
20:13:47	{Equivalent to '20:13:47'(ref)}
23:36:39	4
15:41:43	{Equivalent to '15:40:42'(ref)}


<<<< (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} = 0) ]

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



[ Contents of %cb2hard_linking (#{keys} = 0) ]

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



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

Indx_cblk_A	indx_cblk_B

2	0


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

[ For the 1 th pair: (2, 0) ]


{ The representative path is: 2  -> 0 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	11	12	8	8	15	0,1,2,3,4,5,6,7	0,1,2,3,4,5,6,7
2nd(reconstructed)	0	1	-1	-1	15	0,1,2,3,4,5,6,7	0,1,2,3,4,5,6,7


( Errors associated with the c-blocks )

Subject_c-block	Type	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(???)	15:11:12:X	15:4:4:X
2nd(reconstructed)	Merge(same-type)	15:0:0:X/15:4:4:X	15:2:4:X


