<<<<< 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 = 56 ,
#{Sites in the segment}_rec = 40 .


<< 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)     00000000001111111111222222222233333333334444444444555555
               01234567890123456789012345678901234567890123456789012345
                                                                       
seq0000        ACGAACCTGGCGTCTCCCAGGA----------------GGGC-----------AA-
seq0001        ACGAACCTGGCGTCTCCCAGGA----------------GGGC-----------AA-
seq0002        ACGAACCTAGCGTCTCCCAGGA----------------GAGG-----------AA-
seq0003        ACGAACCTGGCGTCTCCTAGGA----------------GAGG-----------AA-
seq0004        ACGAACCTGGCGTCTCCTAGGA----------------GAGG-----------AA-
seq0005        ACGAACCAGGCGTCTCCCAGG------------------AGC-----------AA-
seq0006        ACGAACCAGGCGTCTCCCAGG------------------AGC-----------AA-
seq0007        ATGAACCAGGCGTCTCCCAGG------------------AGC-----------AA-
seq0008        ACGAAA---------CCCAGTATCGGCCTGATTCGTGCGGGC-----------AAG
seq0009        ACGAAACTGGCTTCTCCAAGGA----------------AGGC-----------AA-
seq0013        ------CTGGCTTATCCCTCGA----------------GGGC-----------AA-
seq0014        ACC-ACCTGGCGACTCCCATGG----------------GGGA-----------AA-
seq0015        AGCGATCTGGCTCCTCGTATGA----------------GGGC-----------AA-
seq0018        GCCAACATGGCTTCTCCCAGGA----------------GGGC-----------AA-
seq0020        ACGAACATTGCGTCTC-----------------------GGCAGATAAGACGAAA-


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333
               0123456789012345678901234567890123456789
                                                       
seq0000        ACGA--------ACCTGGCGTCTCCCAGGA----GGGCAA
seq0001        ACGA--------ACCTGGCGTCTCCCAGGA----GGGCAA
seq0002        ACGA--------ACCTAGCGTCTCCCAGGA----GAGGAA
seq0003        ACGA--------ACCTGGCGTCTCCTAGGA----GAGGAA
seq0004        ACGA--------ACCTGGCGTCTCCTAGGA----GAGGAA
seq0005        ACGA--------ACCAGGCGTCTCCCAGGA------GCAA
seq0006        ACGA--------ACCAGGCGTCTCCCAGGA------GCAA
seq0007        ATGA--------ACCAGGCGTCTCCCAGGA------GCAA
seq0008        ACGAAACCCAGTATCGGCCTGATTCGTGCG----GGCAAG
seq0009        ACGA--------AACTGGCTTCTCCAAGGA----AGGCAA
seq0013        --------------CTGGCTTATCCCTCGA----GGGCAA
seq0014        ACC---------ACCTGGCGACTCCCATGG----GGGAAA
seq0015        AGCG--------ATCTGGCTCCTCGTATGA----GGGCAA
seq0018        GCCA--------ACATGGCTTCTCCCAGGA----GGGCAA
seq0020        ACGA--------ACATTGCGTCTCGGCAGATAAGACGAAA


<<<<< 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, -16) .

[ 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

seq0000   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0001   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0002   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0003   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0004   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0005   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4  -15  -15
seq0006   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4  -15  -15
seq0007   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8  -10    -    -    -    -    -    -   -4   -4  -15  -15
seq0008   	    0    0    0    0    0    0   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9    -    -    -    -   -5   -5   -5  -16  -16  -16
seq0009   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0014   	    0    0    0    -    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0015   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0018   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    -    -    -    -   -4   -4   -4   -4  -15  -15
seq0020   	    0    0    0    0    -    -    -    -    -    -    -    -    8    8    8    8    8    8    8    8    8    8    8    8  -15  -15  -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} = 10) >>

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

0	6	39	16	4,5,0	-9,-5,-16	0,0	8
1	12	29	27	8	8	n/a	0,1,2,3,4,9,11,12,13
2	12	23	28	9	8	n/a	14
3	12	28	14	11	8	n/a	5,6,7
4	14	29	20	10	8	n/a	10
5	24	39	28	2	-15	n/a	14
6	29	29	14	3	-10	n/a	5,6,7
7	34	37	27	6	-4	n/a	0,1,2,3,4,9,10,11,12,13
8	36	37	14	7	-4	n/a	5,6,7
9	38	39	27	1	-15	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13



<<<<< 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} = 10) >>>>>


[[ 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	3	1	0	0	0	0
1
2	1	0	0	0	0	0
3	1	0	0	0	0	0
4	0	0	0	0	0	0
5	2	1	0	0	0	0
6	1	1	0	0	0	0
7
8	0	1	0	0	0	0
9


[ Skipped Composite-Blocks (#{cblocks} = 4): 1, 4, 7, 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	41	34	Complex	16:6:14:X/16:55:55:-/16:22:37:-	16:4:11:-
1	Skipped!!(NO_RELEVANT_BRANCH)
2	0	12	12	Complex(???)	27:16:38:-	None
3	0	17	17	Complex(???)	14:21:38:X	None
4	Skipped!!(NO_ASSOCIATED_EVENT(???))
5	0	16	16	Merge(complementary)	27:16:38:-/28:42:52:-	28:30:33:-
6	0	1	1	Shift	14:21:38:X	14:34:35:X
7	Skipped!!(NO_RELEVANT_BRANCH)
8	0	2	2	Complex(???)	None	14:34:35:X
9	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

20:0:5	{Equivalent to '20:0:13'(rec)}
22:3:3	{Equivalent to '22:3:3'(rec)}
16:6:14	0
27:16:38	2,5
14:21:38	3,6
16:22:37	0
28:42:52	5
16:55:55	0


[ Contents of %indel_rec2assoc_cblks ]

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

20:0:13	{Equivalent to '20:0:5'(ref)}
22:3:3	{Equivalent to '22:3:3'(ref)}
16:4:11	0
28:30:33	5
14:34:35	6,8


<<<< (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]

9	=> [5],


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

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

5	=> [9],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 3) ]

Indx_cblk_A	indx_cblk_B

5	2
6	3
6	8


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

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


{ The representative path is: 5  -> 2 }


( 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)	24	39	-15	-15	28	14	0,1,2,3,4,5,6,7,9,10,11,12,13,14
2nd(reconstructed)	12	23	8	8	28	14	14


( 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)	Partial-Merge(?)	27:16:38:-/28:42:52:-	27:16:23:-/28:30:33:-
2nd(reconstructed)	Complex(???)	27:16:23:-/26:4:11:X	None


[ For the 2 th pair: (6, 3) ]

[ For the 3 th pair: (6, 8) ]

