<<<<< 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 = 47 ,
#{Sites in the segment}_rec = 41 .


<< 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)     00000000001111111111222222222233333333334444444
               01234567890123456789012345678901234567890123456
                                                              
seq0000        -----------------------------CGTACACAAAAACG-AAC
seq0001        -----------------------------CGTACACAAAAACG-AAC
seq0002        -----------------------------CGTAGACAAAAACG-AAC
seq0003        -----------------------------CGTAGACAAAAACG-AAC
seq0004        -----------------------------CGTAGACAAAAACG-AAC
seq0005        -----------------------------CGTAGTCGACGACG-CAT
seq0006        -----------------------------CGTAGACGACGTCG-CAC
seq0007        -----------------------------CGTAGACGACGTCG-CAC
seq0008        -----------------------------CGTAGACAAAAACGTTAG
seq0009        -----------------------------CGTAGACAAAAACA-TAG
seq0013        AGAAGC-GAGGAGTTTAAGGCG-----ATCTTAGCCATAAAC--TTG
seq0014        CGTTGC-CAGTCATTTAAGGCG-----AGGCTAGACATAT-C--GTG
seq0015        GGAAGCACAGTAATTTAAGGTGATTCAAGGGTAGACTA---------
seq0018        -----------------------------GGTAGACTAAAAC--GAG
seq0020        -----------------------------GCTAGATAAAAAC--GCG


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333333334
               01234567890123456789012345678901234567890
                                                        
seq0000        CGTACA-CAAAAAC-GAA----------------------C
seq0001        CGTACA-CAAAAAC-GAA----------------------C
seq0002        CGTAGA-CAAAAAC-GAA----------------------C
seq0003        CGTAGA-CAAAAAC-GAA----------------------C
seq0004        CGTAGA-CAAAAAC-GAA----------------------C
seq0005        CGTAGT-CGACGAC-GCA----------------------T
seq0006        CGTAGA-CGACGTC-GCA----------------------C
seq0007        CGTAGA-CGACGTC-GCA----------------------C
seq0008        CGTAGA-CAAAAACGTTA----------------------G
seq0009        CGTAGA-CAAAAAC-ATA----------------------G
seq0013        AGAAGC-GAGGAGT-TTAAGGCGATCTTAGCCATAAACTTG
seq0014        CGTTGC-CAGTCAT-TTAAGGCGAGGCTAGACATAT-CGTG
seq0015        GGAAGCACAGTAAT-TTAAGGTGATTCAAGGG-TAG-ACTA
seq0018        GGTAGA-CTAAAAC-G-A----------------------G
seq0020        GCTAGA-TAAAAAC-G-C----------------------G


<<<<< 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, -6) .

[ 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

seq0000   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0001   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0002   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0003   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0004   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0005   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0006   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0007   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0008   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0009   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -27  -28  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0013   	    0    0    0    0    0    0    -    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -6   -6   -6
seq0014   	    0    0    0    0    0    0    -    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -   -4   -6   -6   -6
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    2    2    2    -    3    3    3    3
seq0018   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -29    -  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6
seq0020   	  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -28  -28  -28  -28    -  -29    -  -28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6



<<<<< 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} = 11) >>

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

0	0	5	29	0	-29	n/a	0,1,2,3,4,5,6,7,8,9,13,14
1	7	13	29	2	-28	n/a	0,1,2,3,4,5,6,7,9,13,14
2	7	17	16	5	-28	n/a	8
3	15	15	19	6	-27	n/a	0,1,2,3,4,5,6,7,9
4	15	37	22	10,9	1,-4	0	10,11
5	15	40	23	11,12,13	1,2,3	0,0	12
6	15	15	29	1	-29	n/a	13,14
7	16	17	19	4	-28	n/a	0,1,2,3,4,5,6,7,9
8	17	17	29	3	-28	n/a	13,14
9	38	40	22	8	-6	n/a	10,11
10	40	40	29	7	-6	n/a	0,1,2,3,4,5,6,7,8,9,13,14



<<<<< 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} = 11) >>>>>


[[ 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	0	0	0
1	0	0	1	0	0	0
2	1	1	0	0	0	0
3	1	0	0	1	0	0
4	0	1	0	0	0	0
5	2	0	0	0	0	0
6	0	1	1	0	0	0
7	0	0	0	2	0	0
8	0	1	0	1	0	0
9	0	0	1	0	0	0
10	0	1	1	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	6	6	Complex(???)	24:0:28:-	None
1	0	7	7	NO_ASSOCIATED_EVENT(???)	19:42:42:-	None
2	0	11	11	Shift(???)	16:43:43:-	16:14:14:-
3	0	1	1	Complex(???)	19:42:42:-	25:16:16:-
4	0	28	23	Complex(???)	None	22:32:32:-
5	0	24	26	Complex(???)	23:38:46:X/23:22:26:-	None
6	0	1	1	Complex(???)	19:42:42:-	25:16:16:-
7	0	2	2	Complex	None	24:18:39:-/25:16:16:-
8	0	1	1	Complex(???)	None	25:16:16:-/24:18:39:-
9	0	3	3	NO_ASSOCIATED_EVENT(???)	23:38:46:X	None
10	0	1	1	Complex(???)	23:38:46:X	24:18:39:-


[ Contents of %indel_ref2assoc_cblks ]

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

24:0:28	0
23:6:6	{Equivalent to '23:6:6'(rec)}
23:22:26	5
23:38:46	5,9,10
21:40:40	None
19:42:42	1,3,6
16:43:43	2


[ Contents of %indel_rec2assoc_cblks ]

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

23:6:6	{Equivalent to '23:6:6'(ref)}
16:14:14	2
25:16:16	3,6,7,8
24:18:39	7,8,10
22:32:32	4
20:36:36	None


<<<< (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]

8	=> [7],


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

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

7	=> [8],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

