<<<<< 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 = 24 ,
#{Sites in the segment}_rec = 22 .


<< 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)     000000000011111111112222
               012345678901234567890123
                                       
seq0000        AGGTT--AGCGCTGCTGAGCGGT-
seq0001        AGGTT--AGCGCTGCTGAGCGGT-
seq0002        AGGTT--AGCGCTGGTGAGCGAT-
seq0003        AGGTT--AGCGCTGCTGAGCGAT-
seq0004        AGGTT--AGCGCTGCTGAGCGAT-
seq0005        AGGTT--AGAGCTGCAAAGCGAT-
seq0006        AGGTT--AGAGCTGCTGAGCGAT-
seq0007        AGGAT--AGAGCTGCTGAGCGAT-
seq0008        AGGTT--AGCGCTGTGGGGCCAT-
seq0009        GCGTT--AGCGCTGCGGGGCCAC-
seq0013        AG-------CGCTGCTGGTCGAT-
seq0014        AGTTG--ACGGCTCCTAAGCGATT
seq0015        CGTTT--ACGGCTGCTGGGCGGT-
seq0018        GGTCT--TACGCTGGGGGGCGAT-
seq0020        ACTTGACACC--------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122
               0123456789012345678901
                                     
seq0000        AGGTTAGCGCTGCTGAGCGG-T
seq0001        AGGTTAGCGCTGCTGAGCGG-T
seq0002        AGGTTAGCGCTGGTGAGCGA-T
seq0003        AGGTTAGCGCTGCTGAGCGA-T
seq0004        AGGTTAGCGCTGCTGAGCGA-T
seq0005        AGGTTAGAGCTGCAAAGCGA-T
seq0006        AGGTTAGAGCTGCTGAGCGA-T
seq0007        AGGATAGAGCTGCTGAGCGA-T
seq0008        AGGTTAGCGCTGTGGGGCCA-T
seq0009        GCGTTAGCGCTGCGGGGCCA-C
seq0013        -----AGCGCTGCTGGTCGA-T
seq0014        AGTTGACGGCTCCTAAGCGATT
seq0015        CGTTTACGGCTGCTGGGCGG-T
seq0018        GGTCTTACGCTGGGGGGCGA-T
seq0020        ACTTGACAC------------C


<<<<< 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, -2) .

[ 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

seq0000   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0001   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0002   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0003   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0004   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0005   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0006   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0007   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0008   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0009   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0013   	    -    -    -    -    -    5    5   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0014   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0015   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0018   	    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1
seq0020   	    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -   12




[INFORMATION] The original $commoner_shift_flank = -2. 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   14   15   16   17   18   19   20   21   22   23

seq0000   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0001   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0002   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0003   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0004   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0005   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0006   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0007   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0008   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0009   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0013   	    -    -    -    -    -    -    -    7    7    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0014   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0018   	    -    -    2    2    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1
seq0020   	    -    -    2    2    2    2    2    2    2    2    2    -    -    -    -    -    -    -    -    -    -    -    -   14



<<<<< 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} = 5) >>

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

0	2	6	27	3	2	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13
1	2	10	28	4	2	n/a	14
2	7	8	20	5	7	n/a	10
3	23	23	27	2	1	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
4	23	23	28	6	14	n/a	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} = 5) >>>>>


[[ 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	0
2	1	1	0	0	0	0
3	1	1	0	0	0	0
4	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 1): 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	9	9	Complex(???)	28:5:6:-	27:11:21:-
2	0	2	2	Shift	20:2:8:X	20:2:6:X
3	0	1	1	Shift	21:23:23:-	21:22:22:-
4	0	1	1	Complex(???)	27:10:22:-	27:11:21:-


[ Contents of %indel_ref2assoc_cblks ]

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

20:2:8	2
28:5:6	1
27:10:22	4
21:23:23	3


[ Contents of %indel_rec2assoc_cblks ]

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

20:2:6	2
27:11:21	1,4
21:22:22	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} = 1) ]

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

0	=> [1],


[ Contents of %cb2hard_linking (#{keys} = 1) ]

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

1	=> [0],


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

Indx_cblk_A	indx_cblk_B

1	4


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

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


{ The representative path is: 1  -> 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)	2	11	2	2	28	0,1,2,3,4,5,6,7,8,9,11,12,13,14	14
2nd(reconstructed)	23	23	12	12	28	14	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)	Merge(complementary)	27:10:22:-/28:5:6:-	27:12:23:-
2nd(reconstructed)	Shift	27:12:23:-	27:11:21:-


