<<<<< 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 = 43 ,
#{Sites in the segment}_rec = 37 .


<< 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)     0000000000111111111122222222223333333333444
               0123456789012345678901234567890123456789012
                                                          
seq0000        -CATTT---AAGGAAATTT-AATGT-ATTACCTAAT----GGT
seq0001        -CATTT---AAGGAAATTT-AATGT-ATTACCTAGT----GGT
seq0002        -CATTT---AAGGAAATTT-AATGTTTTTACCGAGT----GGT
seq0003        -CATTT---AAGGAAATTT-AATGT-TTTACCGAGT----GGT
seq0004        -CATTT---AAGGACATTG-AATGT-TTTACCGAGT----GGT
seq0005        -C--TT---AAGGAAATTT-AATGT-TCTACCTAGT----GGT
seq0006        -C-TTT---AAGGAAATTT-AATGT-TATACCTAGT----GCT
seq0007        -C-TTT---AAGGAAATTT-AATGC-TATACCTAGT----GGT
seq0008        -CATTT---AAGGAAAATT-AATCT-TATACCTAGT----GGG
seq0009        -CATTT---GAGGAAAATA-AATAT-TATTCCCAGT----GGT
seq0013        -AA-TT---AAGGAAAATT-ACCAT-TAGACGTAGT----GGT
seq0014        ATC-TC---AAGGAAACTTAAAGAT-TATACCTACT----TGT
seq0015        -CA-TT---CTGGAAGATT-AAGAT-AAAACCTAGT----GGA
seq0018        -CC-GAACCAA--CAAATT-AATAT-TAAATCTTGC----GGC
seq0020        -CA-TG---AAGGC-------------------AATCCTCCAA


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333
               0123456789012345678901234567890123456
                                                    
seq0000        C-ATTTAAGGA-AATTTAAT-GTATT-ACCTAATGGT
seq0001        C-ATTTAAGGA-AATTTAAT-GTATT-ACCTAGTGGT
seq0002        C-ATTTAAGGA-AATTTAAT-GTTTTTACCGAGTGGT
seq0003        C-ATTTAAGGA-AATTTAAT-GTTTT-ACCGAGTGGT
seq0004        C-ATTTAAGGA-CATTGAAT-GTTTT-ACCGAGTGGT
seq0005        C--TT-AAGGA-AATTTAAT-GTTCT-ACCTAGTGGT
seq0006        C--TTTAAGGA-AATTTAAT-GTTAT-ACCTAGTGCT
seq0007        C--TTTAAGGA-AATTTAAT-GCTAT-ACCTAGTGGT
seq0008        C-ATTTAAGGA-AAATTAAT-CTTAT-ACCTAGTGGG
seq0009        C-ATTTGAGGA-AAATAAAT-ATTAT-TCCCAGTGGT
seq0013        A-ATT-AAGGA-AAATTACC-ATTAG-ACGTAGTGGT
seq0014        ATCTC-AAGGA-AACTTAAAGATTAT-ACCTACTTGT
seq0015        C-ATT-CTGGA-AGATTAAG-ATAAA-ACCTAGTGGA
seq0018        C-CGA-ACCAACAAATTAAT-ATTAA-ATCTTGCGGC
seq0020        C-ATG-AAGGC-AA---------TCC-TCCAA-----


<<<<< 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

seq0000   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0001   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0002   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0003   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0004   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0005   	   -1    -    -   -1   -1    -   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0006   	   -1    -    -    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0007   	   -1    -    -    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0008   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0009   	   -1    -    0    0    0    0   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0013   	   -1    -    0   -1   -1    -   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0014   	    0    0    0   -1   -1    -   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0015   	   -1    -    0   -1   -1    -   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0018   	   -1    -    0   -1   -1    -    0    0    0    0    0   -2   -2   -2   -2   -2   -2   -3   -3   -3    -   -2   -2   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -6   -6   -6
seq0020   	   -1    -    0   -1   -1    -   -3   -3   -3   -3   -3    -  -21  -21    -    -    -    -    -    -    -    -    -  -12  -12  -12    -  -11  -11  -11  -11  -11    -    -    -    -    -



<<<<< 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} = 16) >>

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

0	0	0	29	13	-1	n/a	0,1,2,3,4,6,7,8,9,10,12,13,14
1	0	4	10	15	-1	n/a	5
2	3	4	29	14	-1	n/a	10,11,12,13,14
3	6	10	29	4	-3	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,14
4	6	10	26	17	0	n/a	13
5	11	16	26	10	-2	n/a	13
6	12	16	25	9	-2	n/a	0,1,2,3,4,5,6,7,8,9,10,12
7	12	22	21	11	-2	n/a	11
8	12	13	28	0	-21	n/a	14
9	17	19	27	5	-3	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
10	21	22	27	8	-2	n/a	0,1,3,4,5,6,7,8,9,10,12,13
11	21	33	4	12	-2	n/a	2
12	23	25	27	6	-3	n/a	0,1,3,4,5,6,7,8,9,10,11,12,13
13	23	31	28	1,2	-12,-11	0	14
14	27	33	27	7	-2	n/a	0,1,3,4,5,6,7,8,9,10,11,12,13
15	34	36	27	3	-6	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,13



<<<<< 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} = 16) >>>>>


[[ 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	1	1	0	0	0	0
3	2	1	1	0	0	0
4	2	1	0	0	0	0
5	1	1	0	0	0	0
6	0	0	1	1	0	0
7	1	1	0	0	0	0
8	1	1	0	1	0	0
9	0	0	0	0	0	0
10	0	1	0	0	0	0
11	1	1	0	0	0	0
12	0	1	0	0	0	0
13	1	2	0	0	0	0
14	2	1	0	0	0	0
15	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 1): 9 . ]


[ 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	21:0:0:-	21:1:1:-
1	0	5	5	Shift(???)	10:3:3:X	10:5:5:X
2	0	2	2	Shift	19:3:3:-	19:5:5:-
3	0	5	5	Complex	26:6:8:-/26:11:12:X/27:14:32:-	26:11:11:-
4	0	5	5	Merge(complementary)	26:11:12:X/26:6:8:-	26:11:11:-
5	0	6	6	Complex(???)	26:11:12:X	26:11:11:-
6	0	5	5	Complex(???)	27:14:32:-	26:11:11:-
7	0	11	11	Shift(???)	21:19:19:-	21:20:20:-
8	0	2	2	Complex(???)	27:14:32:-	27:14:22:-/26:11:11:-
9	Skipped!!(NO_ASSOCIATED_EVENT(???))
10	0	2	2	Complex(???)	None	27:14:22:-
11	0	13	13	Shift(???)	4:25:25:-	4:26:26:-
12	0	3	3	Complex(???)	None	27:14:22:-
13	0	8	9	Complex(???)	28:36:39:-	27:14:22:-/27:32:36:-
14	0	7	7	Complex(???)	28:36:39:-/27:14:32:-	27:32:36:-
15	0	3	3	Complex(???)	28:36:39:-	27:32:36:-


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:0	0
14:2:2	{Equivalent to '14:2:2'(rec)}
19:3:3	2
10:3:3	1
26:6:8	3,4
26:11:12	3,4,5
27:14:32	3,6,8,14
21:19:19	7
4:25:25	11
28:36:39	13,14,15


[ Contents of %indel_rec2assoc_cblks ]

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

21:1:1	0
14:2:2	{Equivalent to '14:2:2'(ref)}
19:5:5	2
10:5:5	1
26:11:11	3,4,5,6,8
27:14:22	8,10,12,13
21:20:20	7
4:26:26	11
27:32:36	13,14,15


<<<< (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) ]]

