<<<<< 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 = 74 ,
#{Sites in the segment}_rec = 74 .


<< 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)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---------------------------------------GTAGTCACT-CTTAAGGAGCT
seq0001        ---------------------------------------GTAGTCACT-CTTAAGGAGCT
seq0002        ---------------------------------------GTATTCACT-CTGAAGGAGCT
seq0003        ---------------------------------------ATATTCACT-CTGAAGGAGCT
seq0004        ---------------------------------------ATATTCACT-CTGAAGGAGCT
seq0005        ---------------------------------------ATAGTCACT-CTTAAGGAGCT
seq0006        ---------------------------------------ATAGACAGT-CTTAAAGAGCG
seq0007        ---------------------------------------ATAGTCACT-CTTAAGGAGCT
seq0008        ---------------------------------------ATAGTCAGT-CTT---GAGCT
seq0009        ---------------------------------------ATAGGCGCT-CTTAAGGAGCT
seq0013        ---------------------------------------AAAGTGGCTCCTTAAGCAGCT
seq0014        ---------------------------------------AAAGGCACC-C-TAAGGATTT
seq0015        --------------------------------------T---------------------
seq0018        GAATTCGACGTACCAATTAGCAGGTGCACACATGGTAG-ATAGACACT-CATAAGGAGCT
seq0020        ---------------------------------------TTAGTCACT-ATTAAGGAGCT

(position)     66666666667777
               01234567890123
                             
seq0000        CGATCAAGCGT-AC
seq0001        CGATCAAGCGT-AC
seq0002        CGATCAAGCGT-AC
seq0003        CGATCAATCGT-AC
seq0004        CGATCAATCGT-AC
seq0005        CGCTCAAGCGT-CC
seq0006        CGATCAAGCGT-CC
seq0007        CGATCAA-CGT-CG
seq0008        GTGTGAATCGTTCC
seq0009        ATGTTAATCGTTGC
seq0013        CT-TTAAGCGT-AA
seq0014        GTGTCAAGCGT-CA
seq0015        ----TAAGGAT-TC
seq0018        GTGCGGAGCGT-CC
seq0020        GTTTGAAGCGT-CC


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --------------------------------------GTA--GTCACTCTTAAGGAGCT
seq0001        --------------------------------------GTA--GTCACTCTTAAGGAGCT
seq0002        --------------------------------------GTA--TTCACTCTGAAGGAGCT
seq0003        --------------------------------------ATA--TTCACTCTGAAGGAGCT
seq0004        --------------------------------------ATA--TTCACTCTGAAGGAGCT
seq0005        --------------------------------------ATA--GTCACTCTTAAGGAGCT
seq0006        --------------------------------------ATA--GACAGTCTTAAAGAGCG
seq0007        --------------------------------------ATA--GTCACTCTTAAGGAGCT
seq0008        --------------------------------------ATA--GTCAGTCTT---GAGCT
seq0009        --------------------------------------ATA--GGCGCTCTTAAGGAGCT
seq0013        --------------------------------------AAAGTGGCTC-CTTAAGCAGCT
seq0014        --------------------------------------AAA--GGCAC-CCTAAGGATTT
seq0015        --------------------------------------------------TTAAGGATTC
seq0018        GAATTCGACGTACCAATTAGCAGGTGCACACATGGTAGATA--GACACTCATAAGGAGCT
seq0020        --------------------------------------TTA--GTCACTATTAAGGAGCT

(position)     66666666667777
               01234567890123
                             
seq0000        CGATCAAGCG-TAC
seq0001        CGATCAAGCG-TAC
seq0002        CGATCAAGCG-TAC
seq0003        CGATCAATCG-TAC
seq0004        CGATCAATCG-TAC
seq0005        CGCTCAAGCG-TCC
seq0006        CGATCAAGCG-TCC
seq0007        CGATCAA-CG-TCG
seq0008        GTGTGAATCGTTCC
seq0009        ATGTTAATCGTTGC
seq0013        CTTT-AAGCG-TAA
seq0014        GTGTCAAGCG-TCA
seq0015        --------------
seq0018        GTGCGGAGCG-TCC
seq0020        GTTTGAAGCG-TCC


<<<<< 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   36   37   38   39   40   41   42   43   44   45   46   47   48   49

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



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    -    1    0    0
seq0008   	    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0    0    0    0    -    1    0    0
seq0014   	    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0015   	   12  -13  -13  -13  -13  -13  -13  -13  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0



<<<<< 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} = 8) >>

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

0	38	40	29	2	-1	n/a	0,1,2,3,4,5,6,7,8,9,11,13,14
1	38	47	20	3	-1	n/a	10
2	43	48	29	10	1	n/a	0,1,2,3,4,5,6,7,8,9,13,14
3	43	50	21	11,13,12	1,2,1	0,0	11
4	50	50	23	14	12	n/a	12
5	51	59	23	1,0	-13,-14	0	12
6	62	63	20	4	-1	n/a	10
7	71	71	29	9	1	n/a	0,1,2,3,4,5,6,7,10,11,13,14



<<<<< 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} = 8) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 1): 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	10	10	Complex(???)	20:48:48:-	20:41:42:-
2	0	6	6	Complex(???)	None	24:48:48:X
3	0	8	8	Complex(???)	21:50:50:X	20:41:42:-
4	0	1	1	Complex(???)	23:39:63:X/23:38:38:-	23:38:49:X
5	0	10	9	Complex(???)	23:39:63:X	23:60:73:X
6	0	2	2	Shift	20:62:62:X	20:64:64:X
7	0	1	1	Shift	18:71:71:-	18:70:70:-


[ Contents of %indel_ref2assoc_cblks ]

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

26:0:37	{Equivalent to '26:0:37'(rec)}
23:38:38	4
23:39:63	4,5
20:48:48	1
21:50:50	3
16:52:54	{Equivalent to '16:52:54'(rec)}
20:62:62	6
12:67:67	{Equivalent to '12:67:67'(rec)}
18:71:71	7


[ Contents of %indel_rec2assoc_cblks ]

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

26:0:37	{Equivalent to '26:0:37'(ref)}
23:38:49	4
20:41:42	1,3
24:48:48	2
16:52:54	{Equivalent to '16:52:54'(ref)}
23:60:73	5
20:64:64	6
12:67:67	{Equivalent to '12:67:67'(ref)}
18:70:70	7


<<<< (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]

0	=> [1],


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

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

1	=> [0],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 2) ]

Indx_cblk_A	indx_cblk_B

1	3
4	5


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

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


{ The representative path is: 1  -> 3 }


( 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)	38	47	-1	-1	20	0,1,2,3,4,5,6,7,8,9,10,11,13,14	10
2nd(reconstructed)	43	50	1	1	21	11	11


( 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(???)	20:48:48:-	20:41:41:-
2nd(reconstructed)	Complex	21:50:50:X/20:41:41:-/22:42:42:-	20:41:42:-


[ For the 2 th pair: (4, 5) ]


{ The representative path is: 5  -> 4 }


( 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)	51	59	-13	-14	23	12	12
2nd(reconstructed)	50	50	12	12	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)	Complex(???)	23:39:63:X	23:39:50:X/23:60:73:X
2nd(reconstructed)	Shift	23:39:50:X	23:38:49:X


