<<<<< 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 = 48 ,
#{Sites in the segment}_rec = 44 .


<< 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)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0001        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0002        -ATAC--------CTCTAGTGCACCTCCGCACCGAAC---CAAT-TAA
seq0003        -ATAT--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAA
seq0004        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAA
seq0005        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAA-TAT
seq0006        -ATAC--------CTCTAGGGCACCTCCGCACCGAAC---CAAT-TAT
seq0007        -ATAC--------CTCTAGAGCACCTCCGCACCGAAC---CAGT-TAT
seq0008        -CTCC------ACCCCGAACGCACCTCCGAACCGCAC------T-TGT
seq0009        -GTAC------ACCACCAGCGCATCTGCGTTCTGAAC------T-TGG
seq0013        -ATAC------AC-----------------------------------
seq0014        -ATAG------ACCTCGAGGGCACCTCCGCCCCGTAA------T-TAT
seq0015        AAATC------GCCTCGAGGGCACCTCGGCACCGAACGGT---TATAT
seq0018        -ATACGTTGTGACCTGGAGGGCAGTTACCTACCGAAC------T-TAT
seq0020        -GTAC------ACCTAGAGGGCATCTCCGCACCGAAG------T-TAT


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333333334444
               01234567890123456789012345678901234567890123
                                                           
seq0000        ATA--------CCTCTAGGGCACCTCCGCACCGAACCAA-TTAT
seq0001        ATA--------CCTCTAGGGCACCTCCGCACCGAACCAA-TTAT
seq0002        ATA--------CCTCTAGTGCACCTCCGCACCGAACCAA-TTAA
seq0003        ATA--------TCTCTAGGGCACCTCCGCACCGAACCAA-TTAA
seq0004        ATA--------CCTCTAGGGCACCTCCGCACCGAACCAA-TTAA
seq0005        ATA--------CCTCTAGGGCACCTCCGCACCGAACCAA-ATAT
seq0006        ATA--------CCTCTAGGGCACCTCCGCACCGAACCAA-TTAT
seq0007        ATA--------CCTCTAGAGCACCTCCGCACCGAACCAG-TTAT
seq0008        CTC------CACCCCGAACGCACCTCCGAACCGCAC----TTGT
seq0009        GTA------CACCACCAGCGCATCTGCGTTCTGAAC----TTGG
seq0013        ATA--------------------------------------CAC
seq0014        ATA------GACCTCGAGGGCACCTCCGCCCCGTAA----TTAT
seq0015        AAA-----TCGCCTCGAGGGCACCTCGGCACCGAACGGTTATAT
seq0018        ATACGTTGTGACCTGGAGGGCAGTTACCTACCGAAC----TTAT
seq0020        GTA------CACCTAGAGGGCATCTCCGCACCGAAG----TTAT


<<<<< 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, -4) .

[ 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

seq0000   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0001   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0002   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0003   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0004   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0005   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0006   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0007   	   -1   -1   -1    -    -    -    -    -    -    -    -    7   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4    -   -3   -4   -4   -4
seq0008   	   -1   -1   -1    -    -    -    -    -    -    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -   -3   -4   -4   -4
seq0009   	   -1   -1   -1    -    -    -    -    -    -    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -   -3   -4   -4   -4
seq0013   	   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   37   31   31
seq0014   	   -1   -1   -1    -    -    -    -    -    -    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -   -3   -4   -4   -4
seq0015   	    0    0    0    -    -    -    -    -    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -   -3   -4   -4   -4
seq0020   	   -1   -1   -1    -    -    -    -    -    -    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -   -3   -4   -4   -4




[INFORMATION] The original $commoner_shift_flank = -4. Thus, we will shift the entire reconstructed MSA ...

<< REVISED Output of 'map_shifts_respos_bw_2msas' >>

New ($shift_lf, $shift_rf) = (0, 0) .

[ New 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

seq0000   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0001   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0002   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0003   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0004   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0005   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0006   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0007   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -   11    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    -    1    0    0    0
seq0008   	    -    -    -    -    3    3    3    -    -    -    -    -    -    9    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    1    0    0    0
seq0009   	    -    -    -    -    3    3    3    -    -    -    -    -    -    9    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    1    0    0    0
seq0013   	    -    -    -    -    3    3    3    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   41   35   35
seq0014   	    -    -    -    -    3    3    3    -    -    -    -    -    -    9    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    1    0    0    0
seq0015   	    -    -    -    -    4    4    4    -    -    -    -    -    9    9    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    0    0    0    0    0
seq0018   	    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    1    0    0    0
seq0020   	    -    -    -    -    3    3    3    -    -    -    -    -    -    9    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    1    0    0    0



<<<<< 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} = 9) >>

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

0	4	6	29	2	3	n/a	0,1,2,3,4,5,6,7,8,9,10,11,14
1	4	42	23	7,9,5	4,9,3	0,0	12
2	4	39	26	4	3	n/a	13
3	13	13	29	8	9	n/a	8,9,11,14
4	14	39	29	3	3	n/a	8,9,11,14
5	15	15	15	10	11	n/a	0,1,2,3,4,5,6,7
6	16	39	15	6	3	n/a	0,1,2,3,4,5,6,7
7	44	44	29	1	1	n/a	0,1,2,3,4,5,6,7,8,9,11,13,14
8	45	47	20	12,11	41,35	0	10



<<<<< 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} = 9) >>>>>


[[ 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	2	1	0	1	0	0
2	1	1	0	1	0	0
3
4
5	1	1	0	0	0	0
6	2	0	0	1	0	0
7	1	1	0	0	0	0
8	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 0, 3, 4 . ]


[ 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	40	39	Complex	23:0:0:-/23:37:39:-	23:43:43:-/22:40:42:X
2	0	36	36	Complex(???)	26:5:10:-	26:7:11:-/25:40:42:-
3	Skipped!!(NO_RELEVANT_BRANCH)
4	Skipped!!(NO_RELEVANT_BRANCH)
5	0	1	1	Shift	15:11:12:X	15:13:14:X
6	0	24	24	Complex	15:11:12:X/15:40:42:-	18:40:42:X
7	0	1	1	Shift	23:44:44:-	23:43:43:-
8	0	9	3	Shift	20:13:47:X	20:13:44:X


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:0	1
26:5:10	2
15:11:12	5,6
20:13:47	8
23:37:39	1
15:40:42	6
23:44:44	7


[ Contents of %indel_rec2assoc_cblks ]

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

26:7:11	2
27:12:12	None
22:12:12	None
19:12:12	None
20:13:44	8
15:13:14	5
25:40:42	2
22:40:42	1
18:40:42	6
23:43:43	1,7


<<<< (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} = 3) ]

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

0	=> [2],
3	=> [1],
4	=> [1,2],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

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

1	=> [3,4],
2	=> [0,4],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 2) ]

Indx_cblk_A	indx_cblk_B

5	6
7	1


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

[ For the 1 th pair: (5, 6) ]

[ For the 2 th pair: (7, 1) ]

