<<<<< 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 = 70 ,
#{Sites in the segment}_rec = 60 .


<< 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        -----TGG-C--------------------------------------------------
seq0001        -----TGG-C--------------------------------------------------
seq0002        -----TGG-C--------------------------------------------------
seq0003        -----TGG-C--------------------------------------------------
seq0004        -----TGG-C--------------------------------------------------
seq0005        -----TGG-C--------------------------------------------------
seq0006        -----TGG-C--------------------------------------------------
seq0007        -----TGG-C--------------------------------------------------
seq0008        -----TGG-C--------------------------------------------------
seq0009        CGGCGTGG-C--------------------------------------------------
seq0013        -----TGG-C-TTCCCTGGCACCGTTATAATGAAAG-CGTGTGAA------------GTG
seq0014        -----TGG-C-TTCCCCGTCAACGAATGAGGGGAATACGTGTGAAGGACTTTGCTGAGTG
seq0015        -----TTG-C-TCGCCCGGAACCGTACGAAGGGAACGCATGTGAAG---GTTTCTGACTG
seq0018        -----TGGTC--------------------------------------------------
seq0020        -----TGG-CG-------------------------------------------------

(position)     6666666666
               0123456789
                         
seq0000        ----------
seq0001        ----------
seq0002        ----------
seq0003        ----------
seq0004        ----------
seq0005        -------ACC
seq0006        ----------
seq0007        ----------
seq0008        ----------
seq0009        ----------
seq0013        ATGCGGT---
seq0014        AGGCAGC---
seq0015        ACGCGGT---
seq0018        ----------
seq0020        ----------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TGG--------------------------------------------------------C
seq0001        TGG--------------------------------------------------------C
seq0002        TGG--------------------------------------------------------C
seq0003        TGG--------------------------------------------------------C
seq0004        TGG--------------------------------------------------------C
seq0005        TGGC-----------------------------------------------------ACC
seq0006        TGG--------------------------------------------------------C
seq0007        TGG--------------------------------------------------------C
seq0008        TGG--------------------------------------------------------C
seq0009        CGGC---------------------------------------------------GTGGC
seq0013        TGGCTTCCCTGGCACCGTTATAA-TGAAAGCGTGTGAAG------------TGATGCGGT
seq0014        TGGCTTCCCCGTCAACGAATGAGGGGAATACGTGTGAAGGACTTTGCTGAGTGAGGCAGC
seq0015        TTGCTCGCCCGGAACCGTACGAAGGGAACGCATGTGAAGG---TTTCTGACTGACGCGGT
seq0018        TGGT-------------------------------------------------------C
seq0020        TGGC-------------------------------------------------------G


<<<<< 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, -10) .

[ 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   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   -5   -5   -5   -6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	   -5   -5   -5   -6   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7    -   -6   -6   -6   -6   -6   -6   -7   -7   -7   -7   -7   -7   -7   -7  -19    -    -    -    -    -    -    -    -    -    -    -
seq0014   	   -5   -5   -5   -6   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7
seq0015   	   -5   -5   -5   -6   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7  -10    -    -    -   -7   -7   -7   -7   -7   -7   -7
seq0018   	   -5   -5   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -5   -5   -5   -6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59

seq0000   	    -    -    -    -    -    -    -    -    -   50
seq0001   	    -    -    -    -    -    -    -    -    -   50
seq0002   	    -    -    -    -    -    -    -    -    -   50
seq0003   	    -    -    -    -    -    -    -    -    -   50
seq0004   	    -    -    -    -    -    -    -    -    -   50
seq0005   	    -    -    -    -    -    -    -  -10  -10  -10
seq0006   	    -    -    -    -    -    -    -    -    -   50
seq0007   	    -    -    -    -    -    -    -    -    -   50
seq0008   	    -    -    -    -    -    -    -    -    -   50
seq0009   	    -    -    -    -    -   51   51   51   51   50
seq0013   	    -   -7   -7   -7   -7   -7   -7   -7   -7   -7
seq0014   	   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7
seq0015   	   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7
seq0018   	    -    -    -    -    -    -    -    -    -   50
seq0020   	    -    -    -    -    -    -    -    -    -   49



<<<<< 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} = 11) >>

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

0	0	2	29	8	-5	n/a	0,1,2,3,4,5,6,7,8,10,11,12,14
1	0	3	26	9	-5	n/a	13
2	3	3	29	6	-6	n/a	5,10,11,12,14
3	4	59	22	5	-7	n/a	10,11
4	4	59	23	3,1,4	-7,-10,-7	0,0	12
5	24	29	20	7	-6	n/a	10
6	38	38	20	0	-19	n/a	10
7	55	58	17	12	51	n/a	9
8	57	59	10	2	-10	n/a	5
9	59	59	27	11	50	n/a	0,1,2,3,4,6,7,8,9,13
10	59	59	28	10	49	n/a	14



<<<<< 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} = 11) >>>>>


[[ 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
3	0	0	1	1	0	0
4	0	0	1	1	0	0
5	1	1	0	0	0	0
6	1	1	0	0	0	0
7	1	0	0	1	0	0
8	1	0	0	0	0	0
9	0	0	0	1	0	0
10	1	0	0	1	0	0


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


[ 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	4	4	Complex(???)	26:8:8:-	None
2	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=3))
3	0	56	56	Complex(???)	24:11:66:-	24:4:54:-
4	0	56	56	Complex(???)	24:11:66:-	24:4:54:-
5	0	6	6	Shift	20:36:36:X	20:23:23:X
6	0	1	1	Shift	20:45:56:X	20:39:50:X
7	0	4	4	Complex(???)	17:0:4:-	16:3:58:X
8	0	3	3	Complex(???)	10:67:69:-	None
9	0	1	1	NO_ASSOCIATED_EVENT(???)	None	25:55:58:-
10	0	1	1	Complex(???)	28:10:10:-	25:55:58:-


[ Contents of %indel_ref2assoc_cblks ]

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

17:0:4	7
26:8:8	1
28:10:10	10
24:11:66	3,4
20:36:36	5
20:45:56	6
21:46:48	None
10:67:69	8


[ Contents of %indel_rec2assoc_cblks ]

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

16:3:58	7
13:3:58	None
9:3:58	None
24:4:54	3,4
20:23:23	5
20:39:50	6
21:40:42	None
25:55:58	9,10
15:55:56	None


<<<< (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]

0	=> [1],


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

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

1	=> [0],


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

Indx_cblk_A	indx_cblk_B

3	4


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

[ For the 1 th pair: (3, 4) ]


{ The representative path is: 3  -> 4 }


( 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)	4	59	-7	-7	22	10,11	10,11
2nd(reconstructed)	4	59	-7	-7	23	12	12


( 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)	Complex(???)	24:11:66:-	22:4:10:-/23:60:66:-
2nd(reconstructed)	Complex	23:60:66:-/22:4:10:-/24:11:54:-	24:4:54:-


