<<<<< 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 = 63 ,
#{Sites in the segment}_rec = 55 .


<< 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        -----------------------------CGTACACAAAAACG-AACTTGAATAAATAG-
seq0001        -----------------------------CGTACACAAAAACG-AACTTGAATAAATGG-
seq0002        -----------------------------CGTAGACAAAAACG-AACTTGAATAAATAG-
seq0003        -----------------------------CGTAGACAAAAACG-AACTTGAATAAATAG-
seq0004        -----------------------------CGTAGACAAAAACG-AACTTGAATAAATAG-
seq0005        -----------------------------CGTAGTCGACGACG-CATTTG-ATAA--AG-
seq0006        -----------------------------CGTAGACGACGTCG-CACTTG-ATAA--AG-
seq0007        -----------------------------CGTAGACGACGTCG-CACTTG-ATAA--AG-
seq0008        -----------------------------CGTAGACAAAAACGTTAGTGGTCTAA--AG-
seq0009        -----------------------------CGTAGACAAAAACA-TAGTTGTCTAA--AG-
seq0013        AGAAGC-GAGGAGTTTAAGGCG-----ATCTTAGCCATAAAC--TTGGTGTCAAA--AGA
seq0014        CGTTGC-CAGTCATTTAAGGCG-----AGGCTAGACATAT-C--GTGTTGTCTAA--GG-
seq0015        GGAAGCACAGTAATTTAAGGTGATTCAAGGGTAGACTA---------CTGTCGAA--AG-
seq0018        -----------------------------GGTAGACTAAAAC--GAGTTGTCTAA---G-
seq0020        -----------------------------GCTAGATAAAAAC--GCGATGTATAA---G-

(position)     666
               012
                  
seq0000        AA-
seq0001        AA-
seq0002        AA-
seq0003        AA-
seq0004        AA-
seq0005        AG-
seq0006        AA-
seq0007        AA-
seq0008        CA-
seq0009        GA-
seq0013        GA-
seq0014        GTG
seq0015        GA-
seq0018        CA-
seq0020        CA-


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333444444444455555
               0123456789012345678901234567890123456789012345678901234
                                                                      
seq0000        CGTACACA------------------------AAAACGAACTTGAATAAATAGAA
seq0001        CGTACACA------------------------AAAACGAACTTGAATAAATGGAA
seq0002        CGTAGACA------------------------AAAACGAACTTGAATAAATAGAA
seq0003        CGTAGACA------------------------AAAACGAACTTGAATAAATAGAA
seq0004        CGTAGACA------------------------AAAACGAACTTGAATAAATAGAA
seq0005        CGTAGTCG------------------------ACGACGCATTTG---ATAAAGAG
seq0006        CGTAGACG------------------------ACGTCGCACTTG---ATAAAGAA
seq0007        CGTAGACG------------------------ACGTCGCACTTG---ATAAAGAA
seq0008        CGTAGACA------------------------AAAACGTTAGTG-GTCTAAAGCA
seq0009        CGTAGACA------------------------AAAACATAGTTG--TCTAAAGGA
seq0013        AGAAGCGA-GGAGTTTAAGGCGATCTTAGCCATAAACTTGGTGT--CAAAAGAGA
seq0014        CGTTGCCA-GTCATTTAAGGCGAGGCTAGA-CATATCGTGTTGT--CTAAGGGTG
seq0015        GGAAGCACAGTAATTTAAGGTGATTCAAG--GGTAGACTACTGT---CGAAAGGA
seq0018        GGTAGACT------------------------AAAACGAGTTGT----CTAAGCA
seq0020        GCTAGATA------------------------AAAACGCGATGT----ATAAGCA


<<<<< 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, -8) .

[ 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   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0006   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0007   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -    -   -4   -4   -4
seq0008   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4
seq0009   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6    -    -   -4   -4   -4   -4
seq0013   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
seq0014   	    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5    -   -4   -4   -4   -4   -4   -5   -7   -7   -7   -7   -7   -7   -7    -    -   -5   -5   -5   -5
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    -    -    2    2    2    2    2    2    2    2    2   -7   -7   -7   -7    -    -    -   -4   -4   -4
seq0018   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3
seq0020   	  -29  -29  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -7   -7   -7   -7   -7   -7   -7    -    -    -    -   -3   -3



(position)	   50   51   52   53   54

seq0000   	   -6   -6   -6   -7   -7
seq0001   	   -6   -6   -6   -7   -7
seq0002   	   -6   -6   -6   -7   -7
seq0003   	   -6   -6   -6   -7   -7
seq0004   	   -6   -6   -6   -7   -7
seq0005   	   -4   -6   -6   -7   -7
seq0006   	   -4   -6   -6   -7   -7
seq0007   	   -4   -6   -6   -7   -7
seq0008   	   -4   -6   -6   -7   -7
seq0009   	   -4   -6   -6   -7   -7
seq0013   	   -7   -7   -7   -7   -7
seq0014   	   -7   -7   -8   -8   -8
seq0015   	   -4   -6   -6   -7   -7
seq0018   	   -3   -3   -6   -7   -7
seq0020   	   -3   -3   -6   -7   -7



<<<<< 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} = 21) >>

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

0	0	7	29	0	-29	n/a	0,1,2,3,4,5,6,7,8,9,13,14
1	6	7	22	21	-1	n/a	10,11
2	22	36	22	14	-5	n/a	10,11
3	31	35	21	17	-4	n/a	11
4	31	39	23	23	2	n/a	12
5	32	37	19	12	-5	n/a	0,1,2,3,4,5,6,7,9
6	32	36	29	11	-5	n/a	13,14
7	32	50	16	15,18	-5,-4	0	8
8	37	43	29	3	-7	n/a	10,11,13,14
9	38	52	9	10	-6	n/a	0,1,2,3,4
10	38	43	19	9	-6	n/a	5,6,7,9
11	40	43	23	4	-7	n/a	12
12	46	49	22	13	-5	n/a	10,11
13	46	50	17	19	-4	n/a	9
14	47	50	25	16	-4	n/a	5,6,7,12
15	48	51	29	20	-3	n/a	13,14
16	50	54	20	6	-7	n/a	10
17	50	54	21	5,1	-7,-8	0	11
18	51	52	25	8	-6	n/a	5,6,7,8,9,12
19	52	52	29	7	-6	n/a	13,14
20	53	54	29	2	-7	n/a	0,1,2,3,4,5,6,7,8,9,12,13,14



<<<<< 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} = 21) >>>>>


[[ 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	0	0	1	0	0
1	0	0	1	1	0	0
2	0	1	1	0	0	0
3	1	0	0	1	0	0
4	1	0	1	1	0	0
5	1	0	0	1	0	0
6	0	0	1	1	0	0
7	1	0	0	0	0	0
8	1	1	0	0	0	0
9	1	1	0	0	0	0
10	0	0	0	0	0	0
11	1	0	0	0	0	0
12	0	0	0	1	0	0
13	0	1	0	0	0	0
14	0	0	0	0	0	0
15	1	1	0	0	0	0
16	1	0	1	0	0	0
17	1	0	0	0	0	0
18	0	0	1	0	0	0
19	1	0	0	0	0	0
20	0	0	2	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 2): 10, 14 . ]


[ 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	8	8	Complex(???)	24:0:28:-	23:8:8:-
1	0	2	2	Shift(gap-aligned)(?)	23:6:6:-	23:8:8:-
2	0	15	15	Complex(???)	23:22:26:-	22:29:29:-
3	0	5	5	Complex(???)	21:40:40:X	20:30:30:-
4	0	9	9	Complex(???)	23:38:46:X/24:0:28:-	22:29:29:-
5	0	6	6	Complex(???)	19:42:42:-	24:9:31:-
6	0	5	5	Complex(???)	19:42:42:-	24:9:31:-
7	0	18	19	Complex(???)	16:43:43:-	None
8	0	7	7	Shift	19:42:42:-	19:45:45:-
9	0	15	15	Complex(???)	9:55:56:-	9:44:44:-
10	Skipped!!(NO_ASSOCIATED_EVENT(???))
11	0	4	4	Complex(???)	23:38:46:X	None
12	0	4	4	NO_ASSOCIATED_EVENT(???)	None	23:46:46:X
13	0	5	5	Complex(???)	None	17:45:45:X
14	Skipped!!(NO_ASSOCIATED_EVENT(???))
15	0	4	4	Complex(???)	25:57:57:-	25:46:47:-
16	0	5	5	Complex(???)	20:59:59:-/21:62:62:-	None
17	0	6	5	Complex(???)	21:62:62:-	None
18	0	2	2	NO_ASSOCIATED_EVENT(???)	20:59:59:-	None
19	0	1	1	Complex(???)	25:57:57:-	None
20	0	2	2	Complex	20:59:59:-/21:62:62:-	None


[ Contents of %indel_ref2assoc_cblks ]

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

24:0:28	0,4
23:6:6	1
23:22:26	2
23:38:46	4,11
21:40:40	3
19:42:42	5,6,8
16:43:43	7
14:50:50	None
9:55:56	9
25:57:57	15,19
20:59:59	16,18,20
21:62:62	16,17,20


[ Contents of %indel_rec2assoc_cblks ]

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

23:8:8	0,1
24:9:31	5,6
22:29:29	2,4
20:30:30	3
9:44:44	9
19:45:45	8
17:45:45	13
14:45:46	None
25:46:47	15
23:46:46	12


<<<< (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} = 4) ]

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

6	=> [5],
10	=> [9],
14	=> [7,13],
20	=> [16],


[ Contents of %cb2hard_linking (#{keys} = 5) ]

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

5	=> [6],
7	=> [14],
9	=> [10],
13	=> [14],
16	=> [20],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 3) ]

Indx_cblk_A	indx_cblk_B

8	5
15	19
16	17


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

[ For the 1 th pair: (8, 5) ]

[ For the 2 th pair: (15, 19) ]

[ For the 3 th pair: (16, 17) ]


{ The representative path is: 16  -> 17 }


( 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)	50	54	-7	-7	20	10	0,1,2,3,4,5,6,7,8,9,10,12,13,14
2nd(reconstructed)	50	54	-7	-8	21	11	11


( 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(???)	20:59:59:-/21:62:62:-	21:50:54:X
2nd(reconstructed)	Complex(???)	21:57:62:-	None


