<<<<< 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 = 16 ,
#{Sites in the segment}_rec = 15 .


<< 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)     0000000000111111
               0123456789012345
                               
seq0000        CTA-CGT--ATTA---
seq0001        CTA-CGT--ATTA---
seq0002        CGA-CGT--ATTA---
seq0003        CGA-CGT--ATTA---
seq0004        CGA-CGT--ATTA---
seq0005        CGA-CGT--ATTG---
seq0006        CGA-CGT--ATTG---
seq0007        CGA-CGT--ATTG---
seq0008        AT---GT--ATTA---
seq0009        AG---GT--ATTA---
seq0013        CGA-TCTCCATTC---
seq0014        CGAACGT--ATTT---
seq0015        CGA-CGT--ATTG---
seq0018        CGA-CGG--ATGT---
seq0020        CGT-CGT--CCTGTCG


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111
               012345678901234
                              
seq0000        CTA-CG---T-ATTA
seq0001        CTA-CG---T-ATTA
seq0002        CGA-CG---T-ATTA
seq0003        CGA-CG---T-ATTA
seq0004        CGA-CG---T-ATTA
seq0005        CGA-CG---T-ATTG
seq0006        CGA-CG---T-ATTG
seq0007        CGA-CG---T-ATTG
seq0008        --A-TG---T-ATTA
seq0009        --A-GG---T-ATTA
seq0013        CGATCT---CCATTC
seq0014        CGAACG---T-ATTT
seq0015        CGA-CG---T-ATTG
seq0018        CGA-CG---G-ATGT
seq0020        CGT-CGTCCT-GTCG


<<<<< 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

seq0000   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0001   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0002   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0003   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0004   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0005   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0006   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0007   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0008   	    -    -    2    -    3    0    -    -    -    3    -    2    2    2    2
seq0009   	    -    -    2    -    3    0    -    -    -    3    -    2    2    2    2
seq0013   	    0    0    0   -1   -1   -1    -    -    -    2    2    2    2    2    2
seq0014   	    0    0    0    0    0    0    -    -    -    3    -    2    2    2    2
seq0015   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0018   	    0    0    0    -    0    0    -    -    -    3    -    2    2    2    2
seq0020   	    0    0    0    -    0    0    0   -2   -2   -2    -   -1   -1   -1   -1



<<<<< 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} = 5) >>

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

0	2	4	18	5,8	2,3	0	8,9
1	3	14	20	2,6	-1,2	0	10
2	7	14	28	0,1	-2,-1	0	14
3	9	9	27	7	3	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13
4	11	14	27	4	2	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13



<<<<< 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} = 5) >>>>>


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


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


[ 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	3	Shift	18:2:4:X	18:0:1:X
1	0	9	12	Partial-Neighboring-Branch-Merge(+shift(?))(?)	20:7:8:-/21:3:3:-	20:10:10:-/22:3:3:-
2	0	7	8	Shift(???)	28:13:15:-	28:6:8:-
3	Skipped!!(NO_RELEVANT_BRANCH)
4	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

18:2:4	0
21:3:3	1
20:7:8	1
28:13:15	2


[ Contents of %indel_rec2assoc_cblks ]

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

18:0:1	0
22:3:3	1
28:6:8	2
20:10:10	1


<<<< (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]

4	=> [1],


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

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

1	=> [4],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

