<<<<< 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 = 45 ,
#{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)     000000000011111111112222222222333333333344444
               012345678901234567890123456789012345678901234
                                                            
seq0000        -CATTT---AAGGAAATTT-AATGT-ATTACCTAAT----GGTGT
seq0001        -CATTT---AAGGAAATTT-AATGT-ATTACCTAGT----GGTGT
seq0002        -CATTT---AAGGAAATTT-AATGTTTTTACCGAGT----GGTGG
seq0003        -CATTT---AAGGAAATTT-AATGT-TTTACCGAGT----GGTGT
seq0004        -CATTT---AAGGACATTG-AATGT-TTTACCGAGT----GGTGT
seq0005        -C--TT---AAGGAAATTT-AATGT-TCTACCTAGT----GGTCT
seq0006        -C-TTT---AAGGAAATTT-AATGT-TATACCTAGT----GCTGT
seq0007        -C-TTT---AAGGAAATTT-AATGC-TATACCTAGT----GGTGT
seq0008        -CATTT---AAGGAAAATT-AATCT-TATACCTAGT----GGGAT
seq0009        -CATTT---GAGGAAAATA-AATAT-TATTCCCAGT----GGTAT
seq0013        -AA-TT---AAGGAAAATT-ACCAT-TAGACGTAGT----GGTAT
seq0014        ATC-TC---AAGGAAACTTAAAGAT-TATACCTACT----TGTAT
seq0015        -CA-TT---CTGGAAGATT-AAGAT-AAAACCTAGT----GGAA-
seq0018        -CC-GAACCAA--CAAATT-AATAT-TAAATCTTGC----GGCAT
seq0020        -CA-TG---AAGGC-------------------AATCCTCCAAAT


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333
               0123456789012345678901234567890123456
                                                    
seq0000        CATTTAAGGAAAT-TTAATG-TATTACCTAATGGTGT
seq0001        CATTTAAGGAAAT-TTAATG-TATTACCTAGTGGTGT
seq0002        CATTTAAGGAAAT-TTAATGTTTTTACCGAGTGGTGG
seq0003        CATTTAAGGAAAT-TTAATG-TTTTACCGAGTGGTGT
seq0004        CATTTAAGGACAT-TGAATG-TTTTACCGAGTGGTGT
seq0005        C--TTAAGGAAAT-TTAATG-TTCTACCTAGTGGTCT
seq0006        C-TTTAAGGAAAT-TTAATG-TTATACCTAGTGCTGT
seq0007        C-TTTAAGGAAAT-TTAATG-CTATACCTAGTGGTGT
seq0008        CATTTAAGGAAAA-TTAATC-TTATACCTAGTGGGAT
seq0009        CATTTGAGGAAAA-TAAATA-TTATTCCCAGTGGTAT
seq0013        A-ATTAAGGAAAA-TTACCA-TTAGACGTAGTGGTAT
seq0014        ATCTCAAGGAAACTTAAAGA-TTATACCTACTTGTAT
seq0015        C-ATTCTGGAAGA-TTAAGA-TAAAACCTAGTGG-AA
seq0018        CCGAACCAACAAA-TTAATA-TTAAATCTTGCGGCAT
seq0020        CATGAAGGCAATCCTCCAAA----------------T


<<<<< 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

seq0000   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0001   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0002   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0003   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0004   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0005   	   -1    -    -   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0006   	   -1    -   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0007   	   -1    -   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0008   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0009   	   -1   -1   -1   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0013   	   -1    -    0   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0014   	    0    0    0   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0015   	   -1    -    0   -1   -1   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8    -   -7   -7
seq0018   	   -1   -1   -2   -2   -2   -2   -2   -2   -2   -4   -4   -4   -4    -   -3   -3   -4   -4   -4   -4    -   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -8   -8   -8   -8   -8
seq0020   	   -1   -1   -2   -2   -5   -5   -5   -5   -5  -24  -24  -24  -24  -24  -24  -24  -24  -24  -24  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -8




[INFORMATION] The original $commoner_shift_flank = -8. 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

seq0000   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    7    -    -    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    7    -    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    7    -    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    7    7    7    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    7    -    8    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    8    8    8    7    7    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    7    -    8    7    7    4    4    4    4    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    -    1    1
seq0018   	    -    -    -    -    -    -    -    -    7    7    6    6    6    6    6    6    6    4    4    4    4    -    5    5    4    4    4    4    -    5    4    4    4    4    4    4    4    4    4    4    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    7    7    6    6    3    3    3    3    3  -16  -16  -16  -16  -16  -16  -16  -16  -16  -16  -16    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    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} = 18) >>

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

0	8	12	19	17	7	n/a	0,1,2,3,4,5,6,7,8,9
1	8	8	24	16	7	n/a	10,12
2	8	10	21	19	8	n/a	11
3	8	9	29	14	7	n/a	13,14
4	10	10	24	18	8	n/a	10,12
5	10	16	26	13	6	n/a	13
6	10	16	28	12,3	6,3	0	14
7	11	12	24	15	7	n/a	10,11,12
8	13	20	25	6	4	n/a	0,1,2,3,4,5,6,7,8,9,10,12
9	13	27	21	8	4	n/a	11
10	17	20	26	7	4	n/a	13
11	17	27	28	0	-16	n/a	14
12	22	23	27	10	5	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
13	24	27	27	5	4	n/a	0,1,3,4,5,6,7,8,9,10,12,13
14	24	39	4	9	4	n/a	2
15	29	29	27	11	5	n/a	0,1,3,4,5,6,7,8,9,10,11,12,13
16	30	39	27	4	4	n/a	0,1,3,4,5,6,7,8,9,10,11,12,13
17	43	44	23	2	1	n/a	12



<<<<< 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} = 18) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 4): 12, 13, 15, 16 . ]


[ 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	5	5	Complex(???)	19:3:3:-	None
1	0	1	1	NO_ASSOCIATED_EVENT(???)	None	23:9:9:X
2	0	3	3	Complex(???)	21:0:0:-	None
3	0	2	2	NO_ASSOCIATED_EVENT(???)	19:3:3:-	None
4	0	1	1	Complex(???)	19:3:3:-	23:9:9:X
5	0	7	7	Complex(???)	26:11:12:X/26:6:8:-	None
6	0	10	7	Complex(???)	27:14:32:-	None
7	0	2	2	NO_ASSOCIATED_EVENT(???)	19:3:3:-	None
8	0	8	8	Complex	26:6:8:-	26:21:21:X/19:21:21:X
9	0	15	15	Complex(???)	21:19:19:-	None
10	0	4	4	Complex(???)	26:11:12:X	26:21:21:X
11	0	11	11	Complex(???)	27:14:32:-/28:36:39:-	27:29:43:-
12	Skipped!!(NO_RELEVANT_BRANCH)
13	Skipped!!(NO_RELEVANT_BRANCH)
14	0	16	16	Shift(???)	4:25:25:-	4:28:28:-
15	Skipped!!(NO_RELEVANT_BRANCH)
16	Skipped!!(NO_RELEVANT_BRANCH)
17	0	2	2	Shift	23:44:44:X	23:42:42:X


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:0	2
14:2:2	{Equivalent to '14:9:9'(rec)}
19:3:3	0,3,4,7
10:3:3	{Equivalent to '10:10:10'(rec)}
26:6:8	5,8
26:11:12	5,10
27:14:32	6,11
21:19:19	9
4:25:25	14
28:36:39	11
23:44:44	17


[ Contents of %indel_rec2assoc_cblks ]

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

23:9:9	1,4
20:9:9	None
14:9:9	{Equivalent to '14:2:2'(ref)}
10:10:10	{Equivalent to '10:3:3'(ref)}
26:21:21	8,10
23:21:21	None
20:21:21	None
19:21:21	8
4:28:28	14
27:29:43	11
23:42:42	17


<<<< (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]

3	=> [0],
7	=> [0],
13	=> [9,14],
16	=> [14],


[ Contents of %cb2hard_linking (#{keys} = 3) ]

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

0	=> [3,7],
9	=> [13],
14	=> [13,16],


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

Indx_cblk_A	indx_cblk_B

0	4
6	11


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

[ For the 1 th pair: (0, 4) ]

[ For the 2 th pair: (6, 11) ]

