<<<<< 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 = 14 ,
#{Sites in the segment}_rec = 13 .


<< 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)     00000000001111
               01234567890123
                             
seq0000        -A-GGC-GCTGT--
seq0001        -A-GGC-GCTGT--
seq0002        -A-GGC-GCTGT--
seq0003        -A-GGC-GCTGT--
seq0004        -A-GGC-GCTGT--
seq0005        -A-GCC-GCGGT--
seq0006        -A-GCC-GCGGT--
seq0007        AA-GCCGGCGGT--
seq0008        -AAGCC-GGTGT--
seq0009        -A-GCC-TGTGT--
seq0013        -A-GCT-TGTGT--
seq0014        -A-GAT-T------
seq0015        -A-GCC-TGTGTGA
seq0018        -A-GAC-GGTGT--
seq0020        -A-GAC-GGTAT--


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111
               0123456789012
                            
seq0000        A--GGCGCTGT--
seq0001        A--GGCGCTGT--
seq0002        A--GGCGCTGT--
seq0003        A--GGCGCTGT--
seq0004        A--GGCGCTGT--
seq0005        A--GCCGCGGT--
seq0006        A--GCCGCGGT--
seq0007        AAGCCGGCGGT--
seq0008        AA-GCCGGTGT--
seq0009        A--GCCTGTGT--
seq0013        A--GCTTGTGT--
seq0014        A------GATT--
seq0015        A--GCCTGTGTGA
seq0018        A--GACGGTGT--
seq0020        A--GACGGTAT--


<<<<< 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, -1) .

[ Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12

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




[INFORMATION] The original $commoner_shift_flank = -1. Thus, we will shift the entire reconstructed MSA ...

<< REVISED Output of 'map_shifts_respos_bw_2msas' >>

New ($shift_lf, $shift_rf) = (0, 0) .

[ New Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13

seq0000   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0001   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0002   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0003   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0004   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0005   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0006   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0007   	    -    1    1    0    0    0    0    0    0    0    0    0    -    -
seq0008   	    -    0    0    -    1    1    1    0    0    0    0    0    -    -
seq0009   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0013   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0014   	    -    0    -    -    -    -    -    -    5    5    5    4    -    -
seq0015   	    -    0    -    -    1    1    1    0    0    0    0    0    0    0
seq0018   	    -    0    -    -    1    1    1    0    0    0    0    0    -    -
seq0020   	    -    0    -    -    1    1    1    0    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} = 3) >>

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

0	1	2	12	1	1	n/a	7
1	4	6	29	0	1	n/a	0,1,2,3,4,5,6,8,9,10,12,13,14
2	8	11	21	3,2	5,4	0	11



<<<<< 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} = 3) >>>>>


[[ 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	1	0	0
1	1	1	0	0	0	0
2	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 0):  . ]


[ 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(???)	12:0:0:-	12:3:3:-/11:2:2:X
1	0	3	3	Shift	12:6:6:-	12:3:3:-
2	0	5	4	Shift	21:8:11:X	21:4:7:X


[ Contents of %indel_ref2assoc_cblks ]

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

12:0:0	0
16:2:2	None
12:6:6	1
21:8:11	2
23:12:13	{Equivalent to '23:12:13'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

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

19:2:2	None
17:2:2	None
11:2:2	0
10:2:2	None
9:2:2	None
12:3:3	0,1
21:4:7	2
23:12:13	{Equivalent to '23:12:13'(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

1	0


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

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


{ The representative path is: 0  -> 1 }


( 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)	1	2	1	1	12	7	7
2nd(reconstructed)	4	6	1	1	12	0,1,2,3,4,5,6,8,9,10,12,13,14	0,1,2,3,4,5,6,8,9,10,12,13,14


( 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)	Collapse-of-Independent-Insertions(+shift)(+3)(?)	16:2:2:-/12:0:0:-	19:2:2:-/17:2:2:X/9:2:2:X/10:2:2:X/11:2:2:X
2nd(reconstructed)	Shift	12:6:6:-	12:3:3:-


