<<<<< 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 = 114 ,
#{Sites in the segment}_rec = 81 .


<< 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)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --C-------------------------------AG------------------------
seq0001        --C-------------------------------AG------------------------
seq0002        --C-------------------------------AG------------------------
seq0003        --C-------------------------------AG------------------------
seq0004        --C-------------------------------AG------------------------
seq0005        CTG-------------------------------AG------------------------
seq0006        CTG-------------------------------AG------------------------
seq0007        CTG-------------------------------AG------------------------
seq0008        CTC-------------------------------AG------------------------
seq0009        CTC-------------------------------AG------------------------
seq0013        ACCAGGA------ACATCCCTTCCTCTGTCCCTAAGTGAGTTGTCGAAATAGGCACAGAA
seq0014        GTCAGGA------GTAGCCCCACGTCTGCCCC-AAC------------------------
seq0015        TTTAGGAGACTCTGTAGCCCTACGGCTGTCCC-AGG------------------------
seq0018        TTC-------------------------------AA------------------------
seq0020        TAC-------------------------------TG------------------------

(position)     000000000000000000000000000000000000000011111111111111
               666666666677777777778888888888999999999900000000001111
               012345678901234567890123456789012345678901234567890123
                                                                     
seq0000        ----------TC-GGTAACG--------------------------------TT
seq0001        ----------TC-GGTAACG--------------------------------TT
seq0002        ----------TC-GGTAACG--------------------------------AT
seq0003        ----------TC-GGTAACG--------------------------------AT
seq0004        ----------TGCGGTAACG--------------------------------AT
seq0005        ----------TG-GGTAACG--------------------------------TT
seq0006        ----------TG-GGTAACG--------------------------------CT
seq0007        ----------TG-GGTAACG--------------------------------TT
seq0008        ----------TC-AGTAA----------------------------------TT
seq0009        ----------AC-AGTAACG----------------------------------
seq0013        CAATAGGAAA---------G--------------------------------TT
seq0014        ----------TG-AGTAAGG--------------------------------TT
seq0015        ----------GC-GGTAAGGAGACAACTTTTCTCAGTACATTCACGCCTATTTT
seq0018        ----------TC-GGTAACG--------------------------------TT
seq0020        ----------TC-GGTAACA--------------------------------TT


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        C--AG-----------------------------------------------------T-
seq0001        C--AG-----------------------------------------------------T-
seq0002        C--AG-----------------------------------------------------T-
seq0003        C--AG-----------------------------------------------------T-
seq0004        C--AG-----------------------------------------------------TG
seq0005        CTGAG-----------------------------------------------------T-
seq0006        CTGAG-----------------------------------------------------T-
seq0007        CTGAG-----------------------------------------------------T-
seq0008        CTCAG-----------------------------------------------------T-
seq0009        CTCAG-----------------------------------------------------A-
seq0013        ACCAGGAA------CATCCCTTCCTCTGTCCCTAAG----TGAGTTGTCGAAATAGGCA-
seq0014        GTCAGGAG------TAGCCCCACGTCTGCCCC-AAC----TGAGT---------------
seq0015        TTTAGGAGACTCTGTAGCCCTACGGCTGTCCC-AGGGCGGTAAGGAGAC-AACTTTTCT-
seq0018        TTCAA-----------------------------------------------------T-
seq0020        TACTG-----------------------------------------------------T-

(position)     666666666677777777778
               012345678901234567890
                                    
seq0000        CGGTA-----------ACGTT
seq0001        CGGTA-----------ACGTT
seq0002        CGGTA-----------ACGAT
seq0003        CGGTA-----------ACGAT
seq0004        CGGTA-----------ACGAT
seq0005        GGGTA-----------ACGTT
seq0006        GGGTA-----------ACGCT
seq0007        GGGTA-----------ACGTT
seq0008        CAGTA-----------A--TT
seq0009        CAGTA-----------A--CG
seq0013        CAGAACAATAG---GAAAGTT
seq0014        ---------------AAGGTT
seq0015        CAGTACATTCACGCCTATTTT
seq0018        CGGTA-----------ACGTT
seq0020        CGGTA-----------ACATT


<<<<< 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, -33) .

[ 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   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -2    -    -  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    4    4    4    4    4    4    4    4    4    4
seq0014   	    0    0    0    0    0    0    0   -6    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    -    -    -    -  -30  -30  -31  -31  -31    -    -    -    -    -
seq0015   	    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    0    0    0    0    0    -    0    0    0  -34  -34  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35    -
seq0018   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0  -31  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80

seq0000   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0001   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0002   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0003   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0004   	    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0005   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0006   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0007   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0008   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1    -    -  -33  -33
seq0009   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1    -    -    1    1
seq0013   	    4    4    4    4    4    4    4    4    4    -    5    5    5    5    5    5    5    5    5    5    5    -    -    -    8    8    8    8   -1  -33  -33
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1  -33  -33
seq0015   	  -34  -34  -34  -34  -34  -34  -34  -34  -34    -  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33
seq0018   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33
seq0020   	    -    -    -    -    -    -    -    -  -12    -  -11  -12  -12  -12  -12    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1  -33  -33



<<<<< 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} = 14) >>

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

0	0	0	9	11	-2	n/a	0,1,2,3,4
1	3	4	29	5	-31	n/a	0,1,2,3,4,5,6,7,8,9,13,14
2	7	7	22	10	-6	n/a	10,11
3	36	80	23	1,0,2,4	-34,-35,-34,-33	0,0,0	12
4	40	77	20	18,19,20	4,5,8	0,0	10
5	40	44	21	7,6	-30,-31	0	11
6	58	64	29	8	-12	n/a	0,1,2,3,4,5,6,7,8,9,13,14
7	60	60	29	9	-11	n/a	0,1,2,3,5,6,7,8,9,13,14
8	75	78	21	14	-1	n/a	11
9	76	78	29	12	-1	n/a	0,1,2,3,4,5,6,7,13,14
10	76	76	18	13	-1	n/a	8,9
11	78	78	20	15	-1	n/a	10
12	79	80	29	3	-33	n/a	0,1,2,3,4,5,6,7,8,10,11,13,14
13	79	80	17	17	1	n/a	9



<<<<< 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} = 14) >>>>>


[[ 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	1	0	0
3	1	2	0	0	0	0
4	2	1	0	0	0	0
5	0	1	2	0	0	0
6	0	2	0	0	0	0
7	1	1	0	0	0	0
8	0	1	0	0	0	0
9	0	1	1	0	0	0
10	0	1	1	0	0	0
11	1	0	0	0	0	0
12
13	1	0	1	1	0	0


[ Skipped Composite-Blocks (#{cblocks} = 1): 12 . ]


[ 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	9:0:1:X	9:1:2:X
1	0	2	2	Complex(???)	24:3:33:-	24:5:57:-
2	0	1	1	Shift(gap-aligned)(?)	23:7:12:-	23:8:13:-
3	0	44	45	Complex(???)	23:80:111:-	23:36:39:-/23:71:73:-
4	0	34	38	Complex(???)	20:70:78:X/20:36:69:-	20:49:49:-
5	0	6	5	Complex	20:36:69:-/20:70:78:X	21:45:74:X
6	0	7	7	Complex(???)	None	24:5:57:-/24:65:75:-
7	0	1	1	Shift	6:72:72:-	6:59:59:-
8	0	4	4	Complex(???)	None	21:45:74:X
9	0	3	3	Complex(???)	23:80:111:-	24:65:75:-
10	0	1	1	Complex(???)	16:78:79:X	18:77:78:X
11	0	1	1	Complex(???)	20:70:78:X	None
12	Skipped!!(NO_RELEVANT_BRANCH)
13	0	2	2	Neighboring-branch-Merge(2del)(?)	17:112:113:X/16:78:79:X	18:77:78:X


[ Contents of %indel_ref2assoc_cblks ]

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

9:0:1	0
24:3:33	1
23:7:12	2
20:32:32	{Equivalent to '20:32:32'(rec)}
20:36:69	4,5
20:70:78	4,5,11
6:72:72	7
16:78:79	10,13
23:80:111	3,9
17:112:113	13


[ Contents of %indel_rec2assoc_cblks ]

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

9:1:2	0
24:5:57	1,6
23:8:13	2
20:32:32	{Equivalent to '20:32:32'(ref)}
23:36:39	3
21:45:74	5,8
20:49:49	4
6:59:59	7
24:65:75	6,9
23:71:73	3
18:77:78	10,13


<<<< (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]

12	=> [3],


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

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

3	=> [12],


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

Indx_cblk_A	indx_cblk_B

13	10


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

[ For the 1 th pair: (13, 10) ]


{ The representative path is: 13  -> 10 }


( 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)	79	80	1	1	17	9	9
2nd(reconstructed)	76	76	-1	-1	18	8,9	8,9


( 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(???)	17:112:113:X/16:78:79:X	18:78:78:X
2nd(reconstructed)	Merge(same-type)	18:76:76:X/18:78:78:X	18:77:78:X


