<<<<< 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 = 17 ,
#{Sites in the segment}_rec = 12 .


<< 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)     00000000001111111
               01234567890123456
                                
seq0000        ACCC-----T-------
seq0001        ACCC-----T-------
seq0002        ACAC-----T-------
seq0003        ACAC-----T-------
seq0004        ACAC-----T-------
seq0005        ACCC-----T-------
seq0006        ACCA-----T-------
seq0007        -CCC-----T-------
seq0008        AACC-----T-------
seq0009        ACCTACCCCT-------
seq0013        AACC-----TTCACACA
seq0014        CCCC-----T-------
seq0015        ACCC-----T-------
seq0018        ATCC-----T-------
seq0020        ACGC-----T-------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011
               012345678901
                           
seq0000        A-------CCCT
seq0001        A-------CCCT
seq0002        A-------CACT
seq0003        A-------CACT
seq0004        A-------CACT
seq0005        A-------CCCT
seq0006        A-------CCAT
seq0007        --------CCCT
seq0008        A-------ACCT
seq0009        A-CCTAC-CCCT
seq0013        AACCTTCACACA
seq0014        C-------CCCT
seq0015        A-------CCCT
seq0018        A-------TCCT
seq0020        A-------CGCT


<<<<< 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, -5) .

[ Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11

seq0000   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0001   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0002   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0003   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0004   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0005   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0006   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0007   	    -    -    -    -    -    -    -    -    7    7    7    2
seq0008   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0009   	    0    -    1    1    1    1    1    -    2    2    2    2
seq0013   	    0    0    0    0   -5   -5   -5   -5   -5   -5   -5   -5
seq0014   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0015   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0018   	    0    -    -    -    -    -    -    -    7    7    7    2
seq0020   	    0    -    -    -    -    -    -    -    7    7    7    2



<<<<< 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} = 4) >>

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

0	2	11	17	1,3	1,2	0	9
1	4	11	20	0	-5	n/a	10
2	8	10	29	4	7	n/a	0,1,2,3,4,5,6,7,8,11,12,13,14
3	11	11	29	2	2	n/a	0,1,2,3,4,5,6,7,8,11,12,13,14



<<<<< 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} = 4) >>>>>


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


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


[ 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	9	10	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+4)(?)	20:10:16:-/17:4:8:-	25:2:6:-/23:2:6:X/21:2:6:X/15:2:6:X/16:2:6:X
1	0	8	8	Incomplete-Collapse-of-Independent-Insertions(+shift(?))(+4)(?)	20:10:16:-/17:4:8:-	25:2:6:-/23:2:6:X/21:2:6:X/15:2:6:X/16:2:6:X/20:7:7:-
2	Skipped!!(NO_RELEVANT_BRANCH)
3	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

12:0:0	{Equivalent to '12:0:0'(rec)}
17:4:8	0,1
20:10:16	0,1


[ Contents of %indel_rec2assoc_cblks ]

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

12:0:0	{Equivalent to '12:0:0'(ref)}
20:1:1	None
25:2:6	0,1
23:2:6	0,1
21:2:6	0,1
16:2:6	0,1
15:2:6	0,1
20:7:7	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]

3	=> [0],


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

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

0	=> [3],


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

Indx_cblk_A	indx_cblk_B



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

