<<<<< 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 = 40 ,
#{Sites in the segment}_rec = 40 .


<< 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)     0000000000111111111122222222223333333333
               0123456789012345678901234567890123456789
                                                       
seq0000        AATCGCTTTACCGCGACTGAGGCTAAC-TTTAGGTT----
seq0001        AATCGCTTTACCGCGACTGAGGCTAAC-TTTAGGTT----
seq0002        AATCGCTTTACCGCGACTGAGGCTAAC-TTTAGGTT----
seq0003        AATCGCTTTACCGCGAATGAGGCTAAC-TTTAGGTT----
seq0004        AATCGCTTTACCGCGACTGAGGCTAAC-TTTAGGTT----
seq0005        AAT------ACCGTGACTTAGGCTAAC-TTACGGTT----
seq0006        AATCGCTTTACCGTGACTTAGGCTAGC-TTAAGGTT----
seq0007        AATCGCTTTACCGTGACTTAGGCTAGC-TTAAGGTT----
seq0008        --CCTCG------GGAATAAGGCTAAC-ATTAGGTC----
seq0009        --TCTCT------GGACTAAGGTTGAAGTTTAGGTAGAGC
seq0013        --TCTCT------GGACTAAGGCTGTC-CTTAGTTC----
seq0014        --TCTTT------GGACTAAGGCGATC-TTTAAGTC----
seq0015        --TCTTT------GTACAAAGGCTAAC-TTTAGGCC----
seq0018        --TCTGT----------------------TTAGGTC----
seq0020        --TATAA-------GACTAAGGCTAAC-TTTAGCTC----


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333
               0123456789012345678901234567890123456789
                                                       
seq0000        AATCGCTTTACCGCGACTGAGGCTAACTT-----TAGGTT
seq0001        AATCGCTTTACCGCGACTGAGGCTAACTT-----TAGGTT
seq0002        AATCGCTTTACCGCGACTGAGGCTAACTT-----TAGGTT
seq0003        AATCGCTTTACCGCGAATGAGGCTAACTT-----TAGGTT
seq0004        AATCGCTTTACCGCGACTGAGGCTAACTT-----TAGGTT
seq0005        AA------TACCGTGACTTAGGCTAACTT-----ACGGTT
seq0006        AATCGCTTTACCGTGACTTAGGCTAGCTT-----AAGGTT
seq0007        AATCGCTTTACCGTGACTTAGGCTAGCTT-----AAGGTT
seq0008        CCT--------CGGGAATAAGGCTAACAT-----TAGGTC
seq0009        TCT--------CTGGACTAAGGTTGAAGTTTAGGTAGAGC
seq0013        TCT--------CTGGACTAAGGCTGTCCT-----TAGTTC
seq0014        TCT--------TTGGACTAAGGCGATCTT-----TAAGTC
seq0015        TCT--------TTGTACAAAGGCTAACTT-----TAGGCC
seq0018        TCT-----------------------GTT-----TAGGTC
seq0020        TAT---------AAGACTAAGGCTAACTT-----TAGCTC


<<<<< 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

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   -1   -1    -    -    -    -    -    4    4    4    4    4    4
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   -1   -1    -    -    -    -    -    4    4    4    4    4    4
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   -1   -1    -    -    -    -    -    4    4    4    4    4    4
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   -1   -1    -    -    -    -    -    4    4    4    4    4    4
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   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0005   	    0    0    -    -    -    -    -    -    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    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    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    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    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0008   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0009   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    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   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0014   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0015   	   -2   -2   -2    -    -    -    -    -    -    -    -    6    6    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    4    4    4    4    4    4
seq0018   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   21   21   -1    -    -    -    -    -    4    4    4    4    4    4
seq0020   	   -2   -2   -2    -    -    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    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} = 8) >>

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

0	0	2	29	0	-2	n/a	8,9,10,11,12,13,14
1	8	8	10	8	6	n/a	5
2	11	12	25	7	6	n/a	8,9,10,11,12
3	12	13	28	9	7	n/a	14
4	26	27	26	10	21	n/a	13
5	27	28	29	1	-1	n/a	0,1,2,3,4,5,6,7,8,10,11,12,14
6	28	28	26	2	-1	n/a	13
7	34	39	29	6	4	n/a	0,1,2,3,4,5,6,7,8,10,11,12,13,14



<<<<< 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} = 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	0	0	0	0
1	1	1	0	0	0	0
2
3	0	0	1	2	0	0
4	0	1	1	0	0	0
5	1	1	0	0	0	0
6	1	0	0	0	0	0
7	1	1	0	0	0	0


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


[ 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	3	3	Complex(???)	15:0:1:-	15:3:10:-
1	0	1	1	Shift	10:3:8:X	10:2:7:X
2	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
3	0	2	2	Complex	25:13:13:-	25:11:11:-/26:12:25:X
4	0	2	2	Complex(???)	25:13:13:-	26:12:25:X
5	0	2	2	Complex(???)	17:27:27:-	17:29:33:-
6	0	1	1	Complex(???)	26:14:28:X	None
7	0	6	6	Complex(???)	17:36:39:-	17:29:33:-


[ Contents of %indel_ref2assoc_cblks ]

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

15:0:1	0
10:3:8	1
15:7:12	None
25:13:13	3,4
26:14:28	6
17:27:27	5
17:36:39	7


[ Contents of %indel_rec2assoc_cblks ]

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

10:2:7	1
15:3:10	0
25:11:11	3
26:12:25	3,4
17:29:33	5,7


<<<< (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} = 2) ]

Indx_cblk_A	indx_cblk_B

3	4
5	7


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

[ For the 1 th pair: (3, 4) ]


{ The representative path is: 3  -> 4 }


( 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)	12	13	7	7	28	14	14
2nd(reconstructed)	26	27	21	21	26	13	13


( 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	25:13:13:-	25:11:11:-/26:12:27:X
2nd(reconstructed)	Complex(???)	27:5:6:-	26:12:25:X


[ For the 2 th pair: (5, 7) ]


{ The representative path is: 5  -> 7 }


( 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)	27	28	-1	-1	17	0,1,2,3,4,5,6,7,8,10,11,12,14	0,1,2,3,4,5,6,7,8,10,11,12,14
2nd(reconstructed)	34	39	4	4	17	0,1,2,3,4,5,6,7,8,10,11,12,13,14	0,1,2,3,4,5,6,7,8,10,11,12,13,14


( 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)	Shift	17:27:27:-	17:29:29:-
2nd(reconstructed)	Merge(same-type)	17:29:29:-/17:36:39:-	17:29:33:-


