<<<<< 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 = 93 ,
#{Sites in the segment}_rec = 72 .


<< 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)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        A-CAG--------------------TAAAC--------TTCACCGCGCAACCCCCCACGA
seq0001        A-CAG--------------------TAAAC--------TTCACCGCGGAACCCCCCACGA
seq0002        A-CAG--------------------TAAAC--------TTCACCG---------CAAGGA
seq0003        A-CAG--------------------TAAAC--------TTCACCG---------CCAGGG
seq0004        A-CAG--------------------TAAAC--------TTCACCG---------CCAGGA
seq0005        A-CAG--------------------TAAAC--------TTCACCACCCAACCCCCCAGGC
seq0006        A-CAG--------------------TAAAC--------TTCACCGCCCAACCCCCCAGGA
seq0007        A-CAG--------------------TAAAC--------TTCACCGCCCAACCCCCCAAGA
seq0008        A-CAG--------------------TTAAC--------TTCATCGCGCATCCCCCAAGGG
seq0009        ACTAG--------------------TCAAC--------AGTACCGCGCAACCTCCCAGGG
seq0013        A-CAGGCTTGAGCTGCTAATGAACGGAAAC--------ATCACCGCGCAGCCCCCAAGTG
seq0014        A-CAGGCACGCACTGCTAA----------T--------TTGACCGGGCAACCCCCAAGGG
seq0015        A-CAG--------------------TAAACTAGACTTCTTCACCGCGGAACCCCCAAGGG
seq0018        ------------------------------------------------------------
seq0020        T-CAA--------------------AAAAC--------TTTACCGGGCAACTCCCAAGCG

(position)     666666666677777777778888888888999
               012345678901234567890123456789012
                                                
seq0000        TTCCAGCATAA--CCAC---------------T
seq0001        TTCCAGCATAA--CCAC---------------T
seq0002        TTCCAGCCTAA--CCAC---------------T
seq0003        TTCCAGCCTAA--CCAC---------------T
seq0004        TTCCAGCCTAA--CCAC---------------T
seq0005        TCCCAGCATAA--CCCC---------------T
seq0006        TGTCAGCATAA--CCCC---------------T
seq0007        TCTCAGCATAA--CCCG---------------T
seq0008        TTCCAGCATAA--CCAC---------------T
seq0009        TTCCAGCATAA--CCAC---------------T
seq0013        TTCCAGCATAAGGCCAC---------------T
seq0014        TTCCTGCATAA--CCAC---------------G
seq0015        TTACGTCAAAA--CCAC---------------T
seq0018        -------ATCA--CCACCCTGTTTGTCTTTGTC
seq0020        -TCCAGTATCA--GCAT---------------T


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        AC-AGTAAA--------CT--------------TCACCGCGCAACCCCCCACGATTCCAG
seq0001        AC-AGTAAA--------CT--------------TCACCGCGGAACCCCCCACGATTCCAG
seq0002        AC-AGTAAA--------CT--------------TCACCGC---------AAGGATTCCAG
seq0003        AC-AGTAAA--------CT--------------TCACCGC---------CAGGGTTCCAG
seq0004        AC-AGTAAA--------CT--------------TCACCGC---------CAGGATTCCAG
seq0005        AC-AGTAAA--------CT--------------TCACCACCCAACCCCCCAGGCTCCCAG
seq0006        AC-AGTAAA--------CT--------------TCACCGCCCAACCCCCCAGGATGTCAG
seq0007        AC-AGTAAA--------CT--------------TCACCGCCCAACCCCCCAAGATCTCAG
seq0008        AC-AGTTAA--------CT--------------TCATCGCGCATCCCCCAAGGGTTCCAG
seq0009        ACTAGTCAA--------CA--------------GTACCGCGCAACCTCCCAGGGTTCCAG
seq0013        AC-AGGCT--TGAGCTGCTAATGAACGGAAACATCACCGCGCAGCCCCCAAGTGTTCCAG
seq0014        AC-AGGCA--CGCACTGCTAAT----------TTGACCGGGCAACCCCCAAGGGTTCCTG
seq0015        AC-AGTAAACTAGACTTCT--------------TCACCGCGGAACCCCCAAGGGTTACGT
seq0018        A--------------------------------TCACC-----ACCC-----TGTTTGTC
seq0020        TC-AAAAAA--------CT--------------TTACCGGGCAACTCCCAAGCGT-CCAG

(position)     666666666677
               012345678901
                           
seq0000        CATAA--CCACT
seq0001        CATAA--CCACT
seq0002        CCTAA--CCACT
seq0003        CCTAA--CCACT
seq0004        CCTAA--CCACT
seq0005        CATAA--CCCCT
seq0006        CATAA--CCCCT
seq0007        CATAA--CCCGT
seq0008        CATAA--CCACT
seq0009        CATAA--CCACT
seq0013        CATAAGGCCACT
seq0014        CATAA--CCACG
seq0015        CAAAA--CCACT
seq0018        TTTGT--C----
seq0020        TATCA--GCATT


<<<<< 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, -21) .

[ 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   48   49

seq0000   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6  -15    -    -    -    -    -    -    -    -    -   -6
seq0003   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6  -15    -    -    -    -    -    -    -    -    -   -6
seq0004   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6  -15    -    -    -    -    -    -    -    -    -   -6
seq0005   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0006   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0007   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0008   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0009   	    0    0    0    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0013   	    0   -1    -    0    0    0    0    0    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0014   	    0   -1    -    0    0    0    0    0    -    -    2    2    2    2    2    2    2    2    2    2    2   -8    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0015   	    0   -1    -    0    0  -20  -20  -20  -20  -20  -20  -20  -20  -20  -20  -20  -20  -20  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0018   	  -67    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -35  -35  -35  -37  -37    -    -    -    -    -  -32  -32  -32  -32    -    -    -
seq0020   	    0   -1    -    0    0  -20  -20  -20  -20    -    -    -    -    -    -    -    -  -12  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71

seq0000   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0001   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0002   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0003   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0004   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0005   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0006   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0007   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0008   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0009   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0013   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6  -21
seq0014   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0015   	   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21
seq0018   	    -    -  -27  -27  -27  -27  -27  -27  -27  -27  -27  -27  -27  -27  -27    -    -  -25    -    -    -    -
seq0020   	   -6   -6   -6   -6   -7    -   -6   -6   -6   -6   -6   -6   -6   -6   -6    -    -   -6   -6   -6   -6  -21



<<<<< 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} = 17) >>

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

0	0	0	26	0	-67	n/a	13
1	1	1	29	18	-1	n/a	0,1,2,3,4,5,6,7,8,10,11,12,14
2	5	8	29	7	-20	n/a	0,1,2,3,4,5,6,7,8,9,14
3	5	18	23	9	-20	n/a	12
4	10	31	20	22	2	n/a	10
5	10	20	21	21	2	n/a	11
6	17	18	29	11,8	-12,-20	0	0,1,2,3,4,5,6,7,8,9,14
7	21	21	21	12	-8	n/a	11
8	32	70	22	17	-6	n/a	10,11
9	33	70	25	16	-6	n/a	0,1,2,3,4,5,6,7,8,9,12
10	33	37	26	2,1	-35,-37	0	13
11	33	54	28	14,13	-6,-7	0	14
12	39	39	8	10	-15	n/a	2,3,4
13	43	46	26	3	-32	n/a	13
14	52	67	26	4,5	-27,-25	0	13
15	56	70	28	15	-6	n/a	14
16	71	71	29	6	-21	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,14



<<<<< 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} = 17) >>>>>


[[ 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	0	0	1	2	0	0
3	1	1	1	1	0	0
4	1	1	0	1	0	0
5	0	0	2	1	0	0
6	0	1	0	1	0	0
7	1	0	0	1	0	0
8	0	1	1	1	0	0
9	1	0	1	0	0	0
10	0	1	0	0	0	0
11	0	1	0	0	0	0
12	1	1	0	0	0	0
13	1	2	0	0	0	0
14	1	2	0	0	0	0
15	0	1	1	0	0	0
16	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	Complex(???)	26:0:66:X	26:1:18:X
1	0	1	1	Shift	17:1:1:-	17:2:2:-
2	0	4	4	Complex	22:5:18:-	23:9:9:-/22:8:8:X
3	0	14	14	Complex(???)	23:30:37:-/22:5:18:-	23:9:9:-/22:19:32:-
4	0	22	22	Complex(???)	20:19:24:-	20:22:31:-/22:8:8:X
5	0	11	11	Complex	20:19:24:-/22:5:18:-	22:8:8:X
6	0	10	2	Complex(???)	None	24:10:16:-/22:19:32:-
7	0	1	1	Complex(???)	21:25:28:X	20:22:31:-
8	0	39	39	Complex(???)	23:30:37:-	22:19:32:-/20:22:31:-
9	0	38	38	Complex(???)	25:60:60:-/26:77:91:-	None
10	0	7	5	Complex(???)	None	26:38:42:X
11	0	23	22	Complex(???)	None	27:55:55:-
12	0	1	1	Shift	8:45:53:X	8:40:48:X
13	0	4	4	Complex(???)	26:77:91:-	26:38:42:X/26:47:51:X
14	0	14	16	Complex(???)	26:77:91:-	26:47:51:X/26:68:71:X
15	0	15	15	Complex(???)	26:77:91:-	27:55:55:-
16	0	1	1	Complex(???)	26:77:91:-	26:68:71:X


[ Contents of %indel_ref2assoc_cblks ]

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

26:0:66	0
17:1:1	1
22:5:18	2,3,5
20:19:24	4,5
21:25:28	7
23:30:37	3,8
8:45:53	12
25:60:60	9
20:71:72	{Equivalent to '20:65:66'(rec)}
26:77:91	9,13,14,15,16


[ Contents of %indel_rec2assoc_cblks ]

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

26:1:18	0
17:2:2	1
22:8:8	2,4,5
23:9:9	2,3
24:10:16	6
22:19:32	3,6,8
20:22:31	4,7,8
26:38:42	10,13
8:40:48	12
26:47:51	13,14
27:55:55	11,15
20:65:66	{Equivalent to '20:71:72'(ref)}
26:68:71	14,16


<<<< (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} = 0) ]

Indx_cblk_A	indx_cblk_B



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

