<<<<< 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 = 58 ,
#{Sites in the segment}_rec = 35 .


<< 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)     0000000000111111111122222222223333333333444444444455555555
               0123456789012345678901234567890123456789012345678901234567
                                                                         
seq0000        ------------------------------GATG-T----------------------
seq0001        ------------------------------GATG-T----------------------
seq0002        ------------------------------GATG-T----------------------
seq0003        ------------------------------GATG-T----------------------
seq0004        ------------------------------GATG-T----------------------
seq0005        ------------------------------GATGCT----------------------
seq0006        ------------------------------GATGCT----------------------
seq0007        ------------------------------GATGCT----------------------
seq0008        ------------------------------GACG-C----------------------
seq0009        ------------------------------GACG-C----------------------
seq0013        ------------------------------GACG-C----------------------
seq0014        GTGCTCACATGACCAAGCAGACATTTGATGGACG-T----------------------
seq0015        ------------------------------GACG-TGCACTGAACTGCTAGGAATTCA
seq0018        ------------------------------GTCG-T----------------------
seq0020        ------------------------------GAGG-T----------------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333
               01234567890123456789012345678901234
                                                  
seq0000        GATG------------------------------T
seq0001        GATG------------------------------T
seq0002        GATG------------------------------T
seq0003        GATG------------------------------T
seq0004        GATG------------------------------T
seq0005        GATG-----------------------------CT
seq0006        GATG-----------------------------CT
seq0007        GATG-----------------------------CT
seq0008        GACG------------------------------C
seq0009        GACG------------------------------C
seq0013        GACG------------------------------C
seq0014        GTGCTCACATGACCAAGCAGACATTTGATGGACGT
seq0015        GACGTGCACTGAACTGCTAGGAATT--------CA
seq0018        GTCG------------------------------T
seq0020        GAGG------------------------------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, -23) .

[ 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

seq0000   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0001   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0002   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0003   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0004   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0005   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1
seq0006   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1
seq0007   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1
seq0008   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0009   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0013   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1
seq0015   	  -30  -30  -30  -30  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -  -23  -23
seq0018   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1
seq0020   	  -30  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -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	3	29	1	-30	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13,14
1	4	34	23	0,2	-31,-23	0	12
2	33	34	14	4	-1	n/a	5,6,7
3	34	34	29	3	-1	n/a	0,1,2,3,4,8,9,10,11,13,14



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


[ Skipped Composite-Blocks (#{cblocks} = 1): 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	4	4	Complex(???)	21:0:29:-	20:4:33:X
1	0	23	31	Complex(???)	23:36:57:-	24:4:24:-
2	0	2	2	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	23:36:57:-/14:34:34:-	25:33:33:-/18:33:33:X/9:33:33:X
3	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:29	0
14:34:34	2
23:36:57	1,2


[ Contents of %indel_rec2assoc_cblks ]

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

24:4:24	1
20:4:33	0
21:25:32	None
25:33:33	2
18:33:33	2
9:33:33	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]

3	=> [2],


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

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

2	=> [3],


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

Indx_cblk_A	indx_cblk_B

2	1


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

[ For the 1 th pair: (2, 1) ]


{ The representative path is: 2  -> 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)	33	34	-1	-1	14	5,6,7	0,1,2,3,4,5,6,7,8,9,10,11,13,14
2nd(reconstructed)	4	34	-31	-23	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)	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	23:36:57:-/14:34:34:-	25:33:33:-/18:33:33:X/9:33:33:X
2nd(reconstructed)	Complex	23:33:34:X/23:35:57:-	24:4:24:-


