<<<<< 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 = 20 ,
#{Sites in the segment}_rec = 19 .


<< 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)     00000000001111111111
               01234567890123456789
                                   
seq0000        CAGTGCGT-----GGATTCC
seq0001        CAGTGCGT-----GGATTCC
seq0002        AAGTGCGT-----GGATTGC
seq0003        AAGTGCGT-----GGATTCC
seq0004        AAGTGCGT-----GGATTCC
seq0005        AAGTGGGT-----GGATTCC
seq0006        AAGTGGGT-----GGATTCC
seq0007        AAGTGGGT-----GGATTCC
seq0008        ACGTGCGT-----AG-TTCT
seq0009        ACGGGCGTAATCCAG-TTCC
seq0013        AACTGCTT------GATTGC
seq0014        AAGTTCGA-----AGATTCC
seq0015        -----------------TCC
seq0018        AG-CCCGG-----AACTTCC
seq0020        -------------------A


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111
               0123456789012345678
                                  
seq0000        CAGTGCGTG----GATTCC
seq0001        CAGTGCGTG----GATTCC
seq0002        AAGTGCGTG----GATTGC
seq0003        AAGTGCGTG----GATTCC
seq0004        AAGTGCGTG----GATTCC
seq0005        AAGTGGGTG----GATTCC
seq0006        AAGTGGGTG----GATTCC
seq0007        AAGTGGGTG----GATTCC
seq0008        ACGTGCGT-----AGTTCT
seq0009        ACGGGCGTAATCCAGTTCC
seq0013        AACTGCTT-----GATTGC
seq0014        AAGTTCGAA----GATTCC
seq0015        ----------------TCC
seq0018        A-GCCCGGA----ACTTCC
seq0020        A------------------


<<<<< 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

seq0000   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0001   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0002   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0003   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0004   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0005   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0006   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0007   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0008   	    0    0    0    0    0    0    0    0    -    -    -    -    -    0    0   -1   -1   -1   -1
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1
seq0013   	    0    0    0    0    0    0    0    0    -    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1
seq0018   	    0    -    1    0    0    0    0    0   -5    -    -    -    -   -1   -1   -1   -1   -1   -1
seq0020   	  -19    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



<<<<< 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} = 6) >>

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

0	0	0	28	0	-19	n/a	14
1	2	2	26	6	1	n/a	13
2	8	8	27	1	-5	n/a	0,1,2,3,4,5,6,7,11,13
3	13	18	27	2	-1	n/a	0,1,2,3,4,5,6,7,10,11,13
4	15	18	18	3	-1	n/a	8,9
5	16	18	23	4	-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} = 6) >>>>>


[[ 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	1	0	0
1	0	0	1	2	0	0
2	0	0	1	2	0	0
3
4	1	0	0	0	0	0
5	0	0	0	0	0	0


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


[ 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	1	1	Complex(???)	27:0:18:-	25:1:1:-
1	0	1	1	Complex	25:2:2:-	25:1:1:-/27:2:18:-
2	0	1	1	Complex	17:8:12:-	17:9:12:-/16:8:8:X
3	Skipped!!(NO_RELEVANT_BRANCH)
4	0	4	4	Complex(???)	18:15:15:X	None
5	Skipped!!(NO_ASSOCIATED_EVENT(???))


[ Contents of %indel_ref2assoc_cblks ]

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

27:0:18	0
23:0:16	{Equivalent to '23:0:15'(rec)}
25:2:2	1
17:8:12	2
20:13:13	{Equivalent to '20:8:8'(rec)}
18:15:15	4


[ Contents of %indel_rec2assoc_cblks ]

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

23:0:15	{Equivalent to '23:0:16'(ref)}
25:1:1	0,1
27:2:18	1
20:8:8	{Equivalent to '20:13:13'(ref)}
16:8:8	2
17:9:12	2


<<<< (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} = 0) ]

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



[ Contents of %cb2hard_linking (#{keys} = 0) ]

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



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

Indx_cblk_A	indx_cblk_B

0	1


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

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


{ The representative path is: 0  -> 1 }


( 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)	0	0	-19	-19	28	14	14
2nd(reconstructed)	2	2	1	1	26	13	13


( 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	27:0:18:-	27:1:18:-
2nd(reconstructed)	Complex(???)	25:2:2:-/27:1:18:-	25:1:1:-/27:2:18:-


