<<<<< 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 = 53 ,
#{Sites in the segment}_rec = 38 .


<< 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)     00000000001111111111222222222233333333334444444444555
               01234567890123456789012345678901234567890123456789012
                                                                    
seq0000        ACGAACCTGGCGTCTCCCAGGA----------------GGGC-----------
seq0001        ACGAACCTGGCGTCTCCCAGGA----------------GGGC-----------
seq0002        ACGAACCTAGCGTCTCCCAGGA----------------GAGG-----------
seq0003        ACGAACCTGGCGTCTCCTAGGA----------------GAGG-----------
seq0004        ACGAACCTGGCGTCTCCTAGGA----------------GAGG-----------
seq0005        ACGAACCAGGCGTCTCCCAGG------------------AGC-----------
seq0006        ACGAACCAGGCGTCTCCCAGG------------------AGC-----------
seq0007        ATGAACCAGGCGTCTCCCAGG------------------AGC-----------
seq0008        ACGAAA---------CCCAGTATCGGCCTGATTCGTGCGGGC-----------
seq0009        ACGAAACTGGCTTCTCCAAGGA----------------AGGC-----------
seq0013        ------CTGGCTTATCCCTCGA----------------GGGC-----------
seq0014        ACC-ACCTGGCGACTCCCATGG----------------GGGA-----------
seq0015        AGCGATCTGGCTCCTCGTATGA----------------GGGC-----------
seq0018        GCCAACATGGCTTCTCCCAGGA----------------GGGC-----------
seq0020        ACGAACATTGCGTCTC-----------------------GGCAGATAAGACGA


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333333
               01234567890123456789012345678901234567
                                                     
seq0000        A-CGAACC-------TGGCGTCTCCCAGGA----GGGC
seq0001        A-CGAACC-------TGGCGTCTCCCAGGA----GGGC
seq0002        A-CGAACC-------TAGCGTCTCCCAGGA----GAGG
seq0003        A-CGAACC-------TGGCGTCTCCTAGGA----GAGG
seq0004        A-CGAACC-------TGGCGTCTCCTAGGA----GAGG
seq0005        A-CGAACC-------AGGCGTCTCCCAGGA------GC
seq0006        A-CGAACC-------AGGCGTCTCCCAGGA------GC
seq0007        A-TGAACC-------AGGCGTCTCCCAGGA------GC
seq0008        A-CGAAACCCAGTATCGGCCTGATTCGTGC----GGGC
seq0009        A-CGAAAC-------TGGCTTCTCCAAGGA----AGGC
seq0013        -------C-------TGGCTTATCCCTCGA----GGGC
seq0014        A-CCA-CC-------TGGCGACTCCCATGG----GGGA
seq0015        AGCGA-TC-------TGGCTCCTCGTATGA----GGGC
seq0018        G-CCAACA-------TGGCTTCTCCCAGGA----GGGC
seq0020        A-CGAACA-------TTGCGTCTCGGCAGATAAGACGA


<<<<< 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, -15) .

[ 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

seq0000   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0001   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0002   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0003   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0004   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0005   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4
seq0006   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4
seq0007   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4
seq0008   	    0    -    1    1    1    1    1   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -   -4   -4   -4   -4
seq0009   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0013   	    -    -    -    -    -    -    -    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0014   	    0    -    1    1    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0015   	    0    0    0    0    0    -    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0018   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4
seq0020   	    0    -    1    1    1    1    1    1    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15



<<<<< 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} = 13) >>

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

0	2	7	29	6	1	n/a	0,1,2,3,4,5,6,7,9,13,14
1	2	3	21	8	1	n/a	11
2	2	6	16	10	1	n/a	8
3	6	7	24	7	1	n/a	11,12
4	7	7	20	9	1	n/a	10
5	7	29	16	2	-8	n/a	8
6	15	29	27	11	8	n/a	0,1,2,3,4,9,10,11,12,13
7	15	23	28	12	8	n/a	14
8	15	28	14	13	8	n/a	5,6,7
9	24	37	28	0	-15	n/a	14
10	29	29	14	1	-10	n/a	5,6,7
11	34	37	27	3	-4	n/a	0,1,2,3,4,8,9,10,11,12,13
12	36	37	14	4	-4	n/a	5,6,7



<<<<< 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} = 13) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 3): 4, 6, 11 . ]


[ 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(???)	None	24:5:5:X/23:1:1:-
1	0	2	2	NO_ASSOCIATED_EVENT(???)	22:3:3:X	None
2	0	5	5	Complex(???)	16:6:14:X	None
3	0	2	2	Complex(???)	None	24:5:5:X
4	Skipped!!(NO_ASSOCIATED_EVENT(???))
5	0	23	23	Merge(complementary)(+shift(^2))(??)	16:6:14:X/16:22:37:-	16:8:14:-
6	Skipped!!(NO_RELEVANT_BRANCH)
7	0	9	9	Complex(???)	27:16:38:-	None
8	0	14	14	Complex(???)	14:21:38:X	None
9	0	14	14	Merge(complementary)(+shift(^2))(??)	27:16:38:-/28:42:52:-	28:30:33:-
10	0	1	1	Shift	14:21:38:X	14:34:35:X
11	Skipped!!(NO_RELEVANT_BRANCH)
12	0	2	2	Complex(???)	None	14:34:35:X


[ Contents of %indel_ref2assoc_cblks ]

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

20:0:5	{Equivalent to '20:0:6'(rec)}
22:3:3	1
16:6:14	2,5
27:16:38	7,9
14:21:38	8,10
16:22:37	5
28:42:52	9


[ Contents of %indel_rec2assoc_cblks ]

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

20:0:6	{Equivalent to '20:0:5'(ref)}
23:1:1	0
24:5:5	0,3
16:8:14	5
28:30:33	9
14:34:35	10,12


<<<< (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} = 2) ]

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

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


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

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

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


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 4) ]

Indx_cblk_A	indx_cblk_B

5	2
9	7
10	12
10	8


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

[ For the 1 th pair: (5, 2) ]

[ For the 2 th pair: (9, 7) ]

[ For the 3 th pair: (10, 12) ]


{ The representative path is: 12  -> 10 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	35	37	-4	-4	14	5,6,7	5,6,7
2nd(reconstructed)	29	29	-6	-6	14	5,6,7	5,6,7


( Errors associated with the c-blocks )

Subject_c-block	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift(???)	14:21:38:X	14:29:34:X
2nd(reconstructed)	Shift	14:29:34:X	14:34:35:X


[ For the 4 th pair: (10, 8) ]

