<<<<< 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 = 65 ,
#{Sites in the segment}_rec = 48 .


<< 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        ---------CCGGG-AATACCC---T------------TAAGCTTAGGATC-G----TCC
seq0001        ---------CCGGG-AATACCC---T------------TAAGCTTAGGGTC-G----TCC
seq0002        ---------TTGGG-AATACCC---T------------TAAGCTTAGGCTC-G----TCC
seq0003        ---------TCGGG-AATACCC---T------------AAAGCTTAGGATC-G----TCC
seq0004        ---------TCGGG-AATACCC---T------------AAAGCTTAGGATC-G----TCC
seq0005        ---------CCGGG-AAGACCT---T------------GAAGCTTAGGATC-G----TCC
seq0006        ---------CCGGG-AAGACCC---T------------GAAGCCTAGGATT-G----TCC
seq0007        ---------CCGGG-AAGACCC---T------------GAAGCTTAGGATC-G----TCC
seq0008        ---------ACGGT-AAGACCATA-------------------TTAGGATC-G----TCC
seq0009        TGAGCCGCCAC-----------------------------------------GAGAATCC
seq0013        ---------ACGGT-AAGACCATACG------------TA-GG-----AGC-A----TC-
seq0014        ---------ACGGT-AAGAC-ATACG------------TA-GGTTAGGCTC-G----TCC
seq0015        ---------ACAGT-AAGACTCTACG------------TA-CGTTAGGCTC-G----TCC
seq0018        ---------AAGGT-AAGACTATA--ACGCTATCGCAATAAGGTTAGGAGC-G----TAA
seq0020        ---------A-GGTTAAGACTACAGTACGCTATCGCCAGAAGGTTTCTATCA--------

(position)     66666
               01234
                    
seq0000        TGGTT
seq0001        TGGTT
seq0002        TGATT
seq0003        TGATT
seq0004        TGATT
seq0005        AGGTT
seq0006        AGGTT
seq0007        AGGTT
seq0008        AGATA
seq0009        AGATA
seq0013        -TATT
seq0014        AGATT
seq0015        AGATT
seq0018        TGACT
seq0020        -----


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        CCGGGAATACCCTT-------------AAGCTTAGGATCGTCCTGGTT
seq0001        CCGGGAATACCCTT-------------AAGCTTAGGGTCGTCCTGGTT
seq0002        TTGGGAATACCCTT-------------AAGCTTAGGCTCGTCCTGATT
seq0003        TCGGGAATACCCTA-------------AAGCTTAGGATCGTCCTGATT
seq0004        TCGGGAATACCCTA-------------AAGCTTAGGATCGTCCTGATT
seq0005        CCGGGAAGACCTTG-------------AAGCTTAGGATCGTCCAGGTT
seq0006        CCGGGAAGACCCTG-------------AAGCCTAGGATTGTCCAGGTT
seq0007        CCGGGAAGACCCTG-------------AAGCTTAGGATCGTCCAGGTT
seq0008        ACGGTAAGACCATA-----------------TTAGGATCGTCCAGATA
seq0009        TGAG------------------------CCGCCACGAGAATCCAGATA
seq0013        ACGGTAAGACCATA----------------CGTAGGAGCATC--TATT
seq0014        ACGGTAAGAC-ATA-----------CGTAGGTTAGGCTCGTCCAGATT
seq0015        ACAGTAAGACTCTA-----------CGTACGTTAGGCTCGTCCAGATT
seq0018        AAGGTAAGACTATAACGCTATCGCAATAAGGTTAGGAGCGTAATGACT
seq0020        AGGTTAAGACTACA------GTACGCTATCGCCAGAAGGTTTCTATCA


<<<<< 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, -17) .

[ 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   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0001   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0002   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0003   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0004   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0005   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0006   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0007   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -13  -25    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0008   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0009   	    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   24   24   24   24   24   24   24  -17  -17  -17  -17  -17  -17  -17  -17  -17  -17  -17  -17  -17
seq0013   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    6    6   -6   -6   -7   -7  -12  -12  -12  -13  -17  -17    -    -  -17  -17  -17  -17
seq0014   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10    -  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    1    1  -11  -11  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0015   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    1    1  -11  -11  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0018   	   -9   -9   -9   -9   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -17  -17  -17  -17  -17  -17  -17  -17
seq0020   	   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10  -10  -10  -10  -10    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4




[INFORMATION] The original $commoner_shift_flank = -17. 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   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    4   -8    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    7    7    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   41   41   41   41   41
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    7    7    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   11
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    -    7    7    7    -    -    -    -    -    -    -    -    -    -    -   18   18    6    6    5    5    5    5
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    7    7    -    -    -    -    -    -    -    -    -    -    -   18   18    6    6    5    5    5    5
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    7    7    7    7    7    7    7    7    7    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    7    7    7    7    7    7    7    7    7    7    7    7    7    -    -    -    -    -    -   13   13   13   13   13   13   13   13   13   13   13   13   13



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64

seq0000   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0001   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0002   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0003   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0004   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0005   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0006   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0007   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0008   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0009   	   41   41    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	   11   10   10    5    5    5    4    0    0    -    -    0    0    0    0
seq0014   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0015   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0018   	    5    5    5    5    5    5    4    0    0    0    0    0    0    0    0
seq0020   	   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13



<<<<< 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	17	21	27	12	8	n/a	0,1,2,3,4,5,6,7,8,10,11,12,13
1	17	17	28	13	8	n/a	14
2	17	20	17	17	17	n/a	9
3	18	64	28	10,16	7,13	0	14
4	22	28	15	11	7	n/a	0,1,2,3,4,5,6,7
5	22	30	27	9	7	n/a	8,10,11,12,13
6	29	30	15	2,0	4,-8	0	0,1,2,3,4,5,6,7
7	31	55	26	3	5	n/a	13
8	42	45	24	18,8	18,6	0	11,12
9	44	55	15	5	5	n/a	0,1,2,3,4,5,6,7
10	45	51	17	20	41	n/a	9
11	46	55	24	4	5	n/a	11,12
12	47	52	20	19,15,14	23,11,10	0,0	10
13	48	55	16	7	5	n/a	8
14	53	55	20	6	5	n/a	10
15	56	56	27	1	4	n/a	0,1,2,3,4,5,6,7,8,10,11,12,13



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


[ Skipped Composite-Blocks (#{cblocks} = 2): 0, 5 . ]


[ 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	1	1	Complex(???)	27:10:10:-	None
2	0	4	4	Complex(???)	17:0:8:-	17:21:30:X
3	0	41	47	Complex	27:10:10:-/27:52:64:-/28:51:51:-/28:14:14:-	None
4	0	7	7	Complex(???)	15:22:23:X	None
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	14	2	Complex	19:24:24:X/18:25:42:X	19:42:43:X
7	0	25	25	Complex	26:24:25:X/28:51:51:-/25:26:37:X	26:31:36:-
8	0	16	4	Complex(???)	24:40:40:X/19:24:24:X	25:37:41:X/19:42:43:X
9	0	12	12	Complex	None	19:42:43:X/18:44:44:X
10	0	7	7	Complex	17:11:50:X/17:0:8:-	18:44:44:X/16:45:47:X
11	0	10	10	Complex(???)	24:40:40:X	None
12	0	19	6	Shift	20:43:47:X	20:42:46:X
13	0	8	8	Complex	18:25:42:X/17:11:50:X	16:45:47:X
14	0	3	3	Complex(???)	20:43:47:X	None
15	0	1	1	Complex(???)	17:53:56:-	None


[ Contents of %indel_ref2assoc_cblks ]

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

17:0:8	2,10
27:10:10	1,3
17:11:50	10,13
28:14:14	3
21:20:20	{Equivalent to '21:27:27'(rec)}
15:22:23	4
26:24:25	7
19:24:24	6,8
18:25:42	6,13
25:26:37	7
24:40:40	8,11
20:43:47	12,14
28:51:51	3,7
27:52:64	3
17:53:56	15
20:59:60	{Equivalent to '20:59:60'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

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

17:21:30	2
21:27:27	{Equivalent to '21:20:20'(ref)}
26:31:36	7
25:37:41	8
20:42:46	12
19:42:43	6,8,9
18:44:44	9,10
16:45:47	10,13
20:59:60	{Equivalent to '20:59:60'(ref)}


<<<< (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]

5	=> [3],


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

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

3	=> [5],


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

Indx_cblk_A	indx_cblk_B

12	14


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

[ For the 1 th pair: (12, 14) ]

