<<<<< 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 = 36 ,
#{Sites in the segment}_rec = 36 .


<< 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)     000000000011111111112222222222333333
               012345678901234567890123456789012345
                                                   
seq0000        GACAAAAAAACTGT-AGTCACCC-----T-------
seq0001        GACAAAAAAACTGT-AGTCACCC-----T-------
seq0002        GACAAAAAAACTTT-AGTCACAC-----T-------
seq0003        GACAAAAAAACTTT-AGTCACAC-----T-------
seq0004        GACAAAAAAACTTT-AGTAACAC-----T-------
seq0005        GACAAAAAAAGTTT-AGTCACCC-----T-------
seq0006        GACAAAAAAAGTTT-AGTCACCA-----T-------
seq0007        GACAAAATAAGTTT-AGTC-CCC-----T-------
seq0008        GAAAAAAAAATCTG-AGTGAACC-----T-------
seq0009        GACATAAAAATTTT-AGTCACCTACCCCT-------
seq0013        GACAAAAAGCTCTTCCCCCAACC-----TTCACACA
seq0014        ---------GACTTCAGTCCCCC-----T-------
seq0015        GACGAAAAACACTTCAGTCACCC-----T-------
seq0018        GCCAAAAAGACCTT-CGGCATCC-----T-------
seq0020        GAGACAAAATATTT-CGTCACGC-----T-------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333
               012345678901234567890123456789012345
                                                   
seq0000        GACAAAAAA-ACTG-------TAGTCA-----CCCT
seq0001        GACAAAAAA-ACTG-------TAGTCA-----CCCT
seq0002        GACAAAAAA-ACTT-------TAGTCA-----CACT
seq0003        GACAAAAAA-ACTT-------TAGTCA-----CACT
seq0004        GACAAAAAA-ACTT-------TAGTAA-----CACT
seq0005        GACAAAAAA-AGTT-------TAGTCA-----CCCT
seq0006        GACAAAAAA-AGTT-------TAGTCA-----CCAT
seq0007        GACAAAATA-AGTT-------TAGTC------CCCT
seq0008        GAAAAAAAA-ATCT-------GAGTGA-----ACCT
seq0009        GACATAAAA-ATTT-------TAGTCACCTACCCCT
seq0013        GACAAAAAGCTCTTCCCCCAACCTTCA-----CACA
seq0014        GA---------CTT-------CAGTCC-----CCCT
seq0015        GACGAAAAACACTT-------CAGTCA-----CCCT
seq0018        GCCAAAAAG-ACCT-------TCGGCA-----TCCT
seq0020        GAGACAAAA-TATT-------TCGTCA-----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, 0) .

[ 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   35

seq0000   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0001   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0002   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0003   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0004   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0005   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0006   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0007   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    -    -    -    -    -    -   12   12   12    7
seq0008   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0009   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    7    7    7    7    7    7    7    7    7
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5    -    -    -    -    -    0    0    0    0
seq0014   	   -9   -9    -    -    -    -    -    -    -    -    -    0    0    0    -    -    -    -    -    -    -    7    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    7    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0018   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7
seq0020   	    0    0    0    0    0    0    0    0    0    -    1    1    1    1    -    -    -    -    -    -    -    8    7    7    7    7    7    -    -    -    -    -   12   12   12    7



<<<<< 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} = 9) >>

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

0	0	1	21	0	-9	n/a	11
1	10	21	29	3,9	1,8	0	0,1,2,3,4,5,6,7,8,9,13,14
2	21	26	24	6	7	n/a	11,12
3	22	26	29	5	7	n/a	0,1,2,3,4,5,6,8,13,14
4	22	25	12	8	7	n/a	7
5	22	35	17	7	7	n/a	9
6	23	26	20	1	-5	n/a	10
7	32	34	29	10	12	n/a	0,1,2,3,4,5,6,7,8,11,12,13,14
8	35	35	29	4	7	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} = 9) >>>>>


[[ 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	0	0	0	0
2
3	1	0	0	0	0	0
4	0	0	0	0	0	0
5	1	1	0	0	0	0
6	1	0	0	0	0	0
7
8


[ Skipped Composite-Blocks (#{cblocks} = 4): 2, 4, 7, 8 . ]


[ 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	2	Shift	21:0:8:X	21:2:10:X
1	0	5	12	Shift	24:14:14:-	24:9:9:-
2	Skipped!!(NO_RELEVANT_BRANCH)
3	0	5	5	Complex(???)	24:14:14:-	None
4	Skipped!!(NO_ASSOCIATED_EVENT(???))
5	0	14	14	Shift(???)	17:23:27:-	17:27:31:-
6	0	4	4	Complex(???)	20:29:35:-	None
7	Skipped!!(NO_RELEVANT_BRANCH)
8	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:8	0
24:14:14	1,3
12:19:19	{Equivalent to '12:26:26'(rec)}
17:23:27	5
20:29:35	6


[ Contents of %indel_rec2assoc_cblks ]

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

21:2:10	0
24:9:9	1
20:14:20	None
12:26:26	{Equivalent to '12:19:19'(ref)}
17:27:31	5


<<<< (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} = 2) ]

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

4	=> [3],
8	=> [5],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

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

3	=> [4],
5	=> [8],


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

Indx_cblk_A	indx_cblk_B

1	3


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

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


{ The representative path is: 3  -> 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)	22	26	7	7	24	0,1,2,3,4,5,6,7,8,13,14	0,1,2,3,4,5,6,8,13,14
2nd(reconstructed)	10	21	1	8	24	0,1,2,3,4,5,6,7,8,9,13,14	0,1,2,3,4,5,6,7,8,9,13,14


( 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(???)	24:14:14:-	24:21:21:-
2nd(reconstructed)	Shift	24:21:21:-	24:9:9:-


