<<<<< 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 = 28 ,
#{Sites in the segment}_rec = 28 .


<< 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)     0000000000111111111122222222
               0123456789012345678901234567
                                           
seq0000        TGCCGTAAGATCATTGCTACCGAGTAT-
seq0001        TGCCGTAAGATCATTGC-----------
seq0002        AGCCGTAAGATCATTGCTACCGAGTAT-
seq0003        AGCCGCAAGATCATTGCTACCGAGTAT-
seq0004        AGCCGTAAGATCATTGCTACCGAGTAT-
seq0005        -------AGAT---TG----CGAGTAT-
seq0006        -------AGAT---TC----CGAGTAG-
seq0007        -------AGAC---TG----CGATTAT-
seq0008        GGCCGTAAGAT---TG----CGGCAAT-
seq0009        GGCCGTAAGAT---TG----GGGCTAA-
seq0013        CTCCGTAAGAT---TG----CGGGTCA-
seq0014        AGCAATATGTT---CG----CGGGTAA-
seq0015        TTACGTAAGAT---TG----CGGGTAA-
seq0018        TGC-GTATGAT---TG----CGAGCCCG
seq0020        TGCCCTAAGAC---TT----CGCGTGA-


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222
               0123456789012345678901234567
                                           
seq0000        TGCCGTAAGATCATTGCTACCG-AGTAT
seq0001        TGCCGTAAGATCATTGC-----------
seq0002        AGCCGTAAGATCATTGCTACCG-AGTAT
seq0003        AGCCGCAAGATCATTGCTACCG-AGTAT
seq0004        AGCCGTAAGATCATTGCTACCG-AGTAT
seq0005        --------------AGATTGCG-AGTAT
seq0006        --------------AGATTCCG-AGTAG
seq0007        --------------AGACTGCG-ATTAT
seq0008        GGCCGTA-------AGATTGCG-GCAAT
seq0009        GGCCGTA-------AGATTGGG-GCTAA
seq0013        CTCCGTA-------AGATTGCG-GGTCA
seq0014        AGCAATA-------TGTTCGCG-GGTAA
seq0015        TTACGTA-------AGATTGCG-GGTAA
seq0018        TG-CGTA-------TGATTGCGAGCCCG
seq0020        TGCCCTA-------AGACTTCG-CGTGA


<<<<< 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

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0008   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0009   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0013   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0014   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0015   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    1    1    1
seq0018   	    0    0    -    1    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    4    4    0    0    -    1    1    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} = 4) >>

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

0	3	3	26	3	1	n/a	13
1	14	17	29	5	7	n/a	5,6,7,8,9,10,11,12,13,14
2	18	19	29	4	4	n/a	5,6,7,8,9,10,11,12,13,14
3	23	27	29	2	1	n/a	0,2,3,4,5,6,7,8,9,10,11,12,14



<<<<< 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} = 4) >>>>>


[[ 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	2	0	0	0	0	0
3	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	1	1	Shift	26:3:3:X	26:2:2:X
1	0	4	4	Complex(???)	9:11:13:-	9:7:13:-
2	0	2	2	Complex(???)	9:11:13:-/9:16:19:-	None
3	0	5	5	Shift	26:27:27:-	26:22:22:-


[ Contents of %indel_ref2assoc_cblks ]

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

14:0:6	{Equivalent to '14:0:6'(rec)}
26:3:3	0
9:11:13	1,2
9:16:19	2
2:17:26	{Equivalent to '2:17:27'(rec)}
26:27:27	3


[ Contents of %indel_rec2assoc_cblks ]

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

14:0:6	{Equivalent to '14:0:6'(ref)}
26:2:2	0
9:7:13	1
2:17:27	{Equivalent to '2:17:26'(ref)}
26:22:22	3


<<<< (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	2


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

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


{ The representative path is: 1  -> 2 }


( 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)	10	13	3	3	9	5,6,7,8,9,10,11,12,13,14	5,6,7,8,9,10,11,12,13,14
2nd(reconstructed)	14	19	4	4	9	5,6,7,8,9,10,11,12,13,14	5,6,7,8,9,10,11,12,13,14


( 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	9:11:13:-	9:7:9:-
2nd(reconstructed)	Merge(same-type)	9:7:9:-/9:16:19:-	9:7:13:-


