<<<<< 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 = 16 .


<< 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        TTCCTTCC-----AG-T
seq0001        TTCCTTCC-----TG-T
seq0002        TTCCTTCC-----AG-T
seq0003        TTCCTTCC-----AG-T
seq0004        TTCCTTCC-----AG-T
seq0005        TTGCATCC-----AG-G
seq0006        TTGCATCC-----AC-G
seq0007        TTCCATCC-----AG-G
seq0008        TTCGATCCTGCTCAG-T
seq0009        TTCGATCC-----ACCG
seq0013        TTCCTTCC-----AG-T
seq0014        TTCCATCC-----AG-T
seq0015        TTCCCTCC-----AG-T
seq0018        ----------------T
seq0020        TTTCATCC-----AG-T


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111
               0123456789012345
                               
seq0000        TTCCTTCCAG-----T
seq0001        TTCCTTCCTG-----T
seq0002        TTCCTTCCAG-----T
seq0003        TTCCTTCCAG-----T
seq0004        TTCCTTCCAG-----T
seq0005        TTGCATCCAG-----G
seq0006        TTGCATCCAC-----G
seq0007        TTCCATCCAG-----G
seq0008        TTCGATCCTGCTCAGT
seq0009        TTCGATCCACC----G
seq0013        TTCCTTCCAG-----T
seq0014        TTCCATCCAG-----T
seq0015        TTCCCTCCAG-----T
seq0018        T---------------
seq0020        TTTCATCCAG-----T


<<<<< 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

seq0000   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0001   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0002   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0003   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0004   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0005   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0006   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0007   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1
seq0009   	    0    0    0    0    0    0    0    0   -5   -5   -5    -    -    -    -   -1
seq0013   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0014   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0015   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -1
seq0018   	  -16    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0   -5   -5    -    -    -    -    -   -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} = 4) >>

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

0	0	0	26	0	-16	n/a	13
1	8	9	29	1	-5	n/a	0,1,2,3,4,5,6,7,10,11,12,14
2	8	10	17	2	-5	n/a	9
3	15	15	29	3	-1	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,14



<<<<< 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	1	0	0	0	0
1	0	1	2	0	0	0
2	1	0	1	2	0	0
3	0	1	0	0	0	0


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


[ 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	Shift	26:0:14:X	26:1:15:X
1	0	2	2	Complex	16:8:12:-/17:15:15:-	18:10:10:-
2	0	3	3	Partial-Neighboring-Branch-Merge(2ins)(+overshoot)(?)	17:15:15:-/16:8:12:-	16:11:14:-/18:10:10:-
3	0	1	1	Complex(???)	None	26:1:15:X


[ Contents of %indel_ref2assoc_cblks ]

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

26:0:14	0
16:8:12	1,2
17:15:15	1,2


[ Contents of %indel_rec2assoc_cblks ]

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

26:1:15	0,3
18:10:10	1,2
16:11:14	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} = 1) ]

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

1	=> [2],


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

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

2	=> [1],


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

Indx_cblk_A	indx_cblk_B

0	3


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

[ For the 1 th pair: (0, 3) ]


{ The representative path is: 3  -> 0 }


( 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)	15	15	-1	-1	26	0,1,2,3,4,5,6,7,8,9,10,11,12,14	0,1,2,3,4,5,6,7,8,9,10,11,12,14
2nd(reconstructed)	0	0	-16	-16	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)	Complex(???)	None	26:16:16:-/26:0:15:X
2nd(reconstructed)	Merge(complementary)(+shift)(?)	26:0:15:X/26:16:16:-	26:1:15:X


