<<<<< 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 = 43 ,
#{Sites in the segment}_rec = 43 .


<< 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)     0000000000111111111122222222223333333333444
               0123456789012345678901234567890123456789012
                                                          
seq0000        AGGACATACT-----------CTTTCTTTTGTGCAT-GGCCGA
seq0001        AGGACACACT-----------CTTTCTTTTGTGCAT-GGCCGA
seq0002        AGGACACACT-----------CTTTCTTTTGTGCAT-GACCGA
seq0003        AGGACACACT-----------CTTTATTTTGTGCAT-GACCGA
seq0004        AGGACACACT-----------CTTTATTTTGTGCAT-GACCGA
seq0005        AGGGCCCACT-----------CATGCTTTATTGCCT-GACCGG
seq0006        AGGCCGCACT-----------CATTCTTTAGTGCCT-CACCGG
seq0007        AGGTCGCACT-----------CCTTCTTTAGTGCCT-CACCGG
seq0008        AGGCCACACT-----------CATTGTTCGGAGCCT-GA----
seq0009        AGGCCACACT-----------CTAAATTCTGAACCGAGCCCGA
seq0013        CGG------T-----------CTTCCTTCTGATCTT-GACCGA
seq0014        AAG------T-----------CTTCCTTCTGGACCT-GACCGC
seq0015        ------------------------------GA------ACCGA
seq0018        AGGCCAAAGTGCGGTTTTATGCTTCCTTCTGTTCCT-GGCCGA
seq0020        ACCCCCATCT-----------CTTCCCTCTGCTCCT-GAGCGC


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333444
               0123456789012345678901234567890123456789012
                                                          
seq0000        AGGACATACT-----------CTTTCTTTTGTGCA-TGGCCGA
seq0001        AGGACACACT-----------CTTTCTTTTGTGCA-TGGCCGA
seq0002        AGGACACACT-----------CTTTCTTTTGTGCA-TGACCGA
seq0003        AGGACACACT-----------CTTTATTTTGTGCA-TGACCGA
seq0004        AGGACACACT-----------CTTTATTTTGTGCA-TGACCGA
seq0005        AGGGCCCACT-----------CATGCTTTATTGCC-TGACCGG
seq0006        AGGCCGCACT-----------CATTCTTTAGTGCC-TCACCGG
seq0007        AGGTCGCACT-----------CCTTCTTTAGTGCC-TCACCGG
seq0008        AGGCCACACT-----------CATTGTTCGGAGCC-----TGA
seq0009        AGGCCACACT-----------CTAAATTCTGAACCGAGCCCGA
seq0013        CGGT-----------------CTTCCTTCTGATCT-TGACCGA
seq0014        AAGT-----------------CTTCCTTCTGGACC-TGACCGC
seq0015        G------------------------------------AACCGA
seq0018        AGGCCAAAGTGCGGTTTTATGCTTCCTTCTGTTCC-TGGCCGA
seq0020        ACCCCCATCT-----------CTTCCCTCTGCTCC-TGAGCGC


<<<<< 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

seq0000   	    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    0    0    0    0    0    0
seq0001   	    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    0    0    0    0    0    0
seq0002   	    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    0    0    0    0    0    0
seq0003   	    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    0    0    0    0    0    0
seq0004   	    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    0    0    0    0    0    0
seq0005   	    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    0    0    0    0    0    0
seq0006   	    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    0    0    0    0    0    0
seq0007   	    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    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    5    4    4
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    0    0    0    0    0    0    0    0
seq0013   	    0    0    0   -6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0
seq0014   	    0    0    0   -6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0
seq0015   	  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    6    0    0    0    0    0
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    -    1    0    0    0    0    0    0
seq0020   	    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    0    0    0    0    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} = 5) >>

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

0	0	0	23	0	-30	n/a	12
1	3	3	22	1	-6	n/a	10,11
2	36	36	29	3	1	n/a	0,1,2,3,4,5,6,7,10,11,13,14
3	37	37	23	6	6	n/a	12
4	40	42	16	5,4	5,4	0	8



<<<<< 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} = 5) >>>>>


[[ 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	0	1	1	0	0
2	0	0	1	2	0	0
3	1	1	0	0	0	0
4	1	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	Complex(???)	23:0:29:X	23:1:36:X
1	0	1	1	Shift(gap-aligned)(?)	24:3:8:X	24:4:9:X
2	0	1	1	Complex	17:36:36:-	17:35:35:-/16:36:39:X
3	0	1	1	Complex(???)	23:32:37:X	23:1:36:X
4	0	4	3	Shift	16:39:42:X	16:36:39:X


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:29	0
24:3:8	1
26:10:20	{Equivalent to '26:10:20'(rec)}
23:32:37	3
17:36:36	2
16:39:42	4


[ Contents of %indel_rec2assoc_cblks ]

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

23:1:36	0,3
24:4:9	1
26:10:20	{Equivalent to '26:10:20'(ref)}
17:35:35	2
16:36:39	2,4


<<<< (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} = 0) ]

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



[ Contents of %cb2hard_linking (#{keys} = 0) ]

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



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

Indx_cblk_A	indx_cblk_B

0	3
4	2


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

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


{ The representative path is: 0  -> 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)	0	0	-30	-30	23	12	12
2nd(reconstructed)	37	37	6	6	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)	Shift	23:0:29:X	23:1:30:X
2nd(reconstructed)	Merge(same-type)	23:1:30:X/23:32:37:X	23:1:36:X


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


{ The representative path is: 4  -> 2 }


( 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)	40	42	5	4	16	8	8
2nd(reconstructed)	36	36	1	1	18	0,1,2,3,4,5,6,7,10,11,13,14	0,1,2,3,4,5,6,7,10,11,13,14


( 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	16:39:42:X	16:35:39:X
2nd(reconstructed)	Complex(???)	17:36:36:-/16:35:39:X	17:35:35:-/16:36:39:X


