<<<<< 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 = 49 ,
#{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)     0000000000111111111122222222223333333333444444444
               0123456789012345678901234567890123456789012345678
                                                                
seq0000        TCCAC--------G-----------------------------CAGCGT
seq0001        TCCAC--------G-----------------------------CAGCGT
seq0002        TCCA---------------------------------------CAGCGT
seq0003        GCCA---------------------------------------CAACGT
seq0004        TCCA---------------------------------------CAGCGT
seq0005        TCGAT--------G-----------------------------CAGCAT
seq0006        TCCAT--------G-----------------------------CAGCAT
seq0007        TCCAT--------G-----------------------------CAGCAT
seq0008        ACCAT--------C-----------------------------CAACAA
seq0009        TCCATAGAAGAACG-----------------------------CACAAG
seq0013        TCCAT--------G-----------------------------CAAC-T
seq0014        TC-AA--------GGTTTGGGCGACCATTACACCTGTTCCCTGCAACAT
seq0015        CCTAA--------G-----------------------------CTA--T
seq0018        CACAA--------G-----------------------------CAACAT
seq0020        TCCAT--------G-----------------------------CAACAT


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444
               012345678901234567890123456789012345678901234567
                                                               
seq0000        ----------------------------TCCACGCAGCGT--------
seq0001        ----------------------------TCCACGCAGCGT--------
seq0002        ----------------------------TCCA--CAGCGT--------
seq0003        ----------------------------GCCA--CAACGT--------
seq0004        ----------------------------TCCA--CAGCGT--------
seq0005        ----------------------------TCGATGCAGCAT--------
seq0006        ----------------------------TCCATGCAGCAT--------
seq0007        ----------------------------TCCATGCAGCAT--------
seq0008        ----------------------------ACCATCCAACAA--------
seq0009        ----------------------------TCCATAGAAGAACGCACAAG
seq0013        ----------------------------TCCATGCAAC---------T
seq0014        TCAAGGTTTGGGCGACCATTACACCTGTTCCCTGCAACAT--------
seq0015        ----------------------------CCTAAGCTAT----------
seq0018        ----------------------------CACAAGCAACAT--------
seq0020        ----------------------------TCCATGCAACAT--------


<<<<< 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, -1) .

[ 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28    -    -   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28    -    -   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28    -    -   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   28   28   28   28   28   28   28   28   28   -1   -1   -1   -1   -1   -1
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9    -    -    -    -    -    -    -    -    -   -1
seq0014   	    0    0   -1   -1   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9  -11    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -




[INFORMATION] The original $commoner_shift_flank = -1. 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

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29    -    -   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   29   29   29   29   29   29   29   29   29    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8    -    -    -    -    -    -    -    -    -    0
seq0014   	    -    1    1    0    0   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8  -10    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -



<<<<< 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	1	2	21	6	1	n/a	11
1	3	40	21	5,3	0,-8	0	11
2	29	33	29	8	29	n/a	0,1,5,6,7,8,10,12,13,14
3	29	32	8	10	29	n/a	2,3,4
4	29	42	17	9	29	n/a	9
5	34	34	29	7	21	n/a	0,1,5,6,7,8,10,12,13,14
6	35	40	29	1	-8	n/a	0,1,2,3,4,5,6,7,8,13,14
7	35	38	20	4	-8	n/a	10
8	35	37	23	2	-8	n/a	12
9	38	38	23	0	-10	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} = 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	1	1	0	0	0	0
1	2	2	0	1	0	0
2
3	0	0	0	0	0	0
4	1	1	0	0	0	0
5
6	0	0	0	0	0	0
7	1	1	1	0	0	0
8	1	0	0	0	0	0
9	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 4): 2, 3, 5, 6 . ]


[ 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	2	2	Complex(???)	21:2:2:X	21:1:28:-
1	0	46	38	Complex	21:2:2:X/21:14:42:-	21:48:48:X/21:1:28:-/20:39:40:X
2	Skipped!!(NO_RELEVANT_BRANCH)
3	Skipped!!(NO_ASSOCIATED_EVENT(???))
4	0	14	14	Complex(???)	17:5:12:-	17:41:47:-
5	Skipped!!(NO_RELEVANT_BRANCH)
6	Skipped!!(NO_ASSOCIATED_EVENT(???))
7	0	4	4	Complex(???)	20:47:47:X/21:14:42:-	20:39:40:X
8	0	3	3	Complex(???)	23:46:47:X	None
9	0	1	1	Complex(???)	23:46:47:X	23:39:48:X


[ Contents of %indel_ref2assoc_cblks ]

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

21:2:2	0,1
8:4:13	{Equivalent to '8:33:34'(rec)}
17:5:12	4
21:14:42	1,7
23:46:47	8,9
20:47:47	7


[ Contents of %indel_rec2assoc_cblks ]

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

21:1:28	0,1
8:33:34	{Equivalent to '8:4:13'(ref)}
23:39:48	9
20:39:40	1,7
17:41:47	4
25:48:48	None
21:48:48	1
16:48:48	None
15:48:48	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]

2	=> [4],


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

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

4	=> [2],


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

Indx_cblk_A	indx_cblk_B

8	9


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

[ For the 1 th pair: (8, 9) ]


{ The representative path is: 8  -> 9 }


( 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	-8	-8	23	12	12
2nd(reconstructed)	38	38	-10	-10	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(???)	23:46:47:X	23:38:40:X
2nd(reconstructed)	Shift	23:38:40:X	23:39:48:X


