<<<<< 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 = 25 ,
#{Sites in the segment}_rec = 25 .


<< 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)     0000000000111111111122222
               0123456789012345678901234
                                        
seq0000        CCGAAGAGTTTGTC-----ATCT-A
seq0001        CCGAAGACTTTGTC-----ATCT-A
seq0002        TCGAAGACTTTGTC-----ATCT-A
seq0003        TCGAAGACTTTGTC-----ATCT-A
seq0004        TCGAAGACTTTGTC-----ATCT-A
seq0005        TCGAAGACTTTGTC-----ATCT-A
seq0006        TCGAAGACTTTGTC-----ATCT-A
seq0007        TCGAAGACTTTGTC-----ATCT-A
seq0008        TAGACCACTTT-TC-----GACT-A
seq0009        TCGAAGACTTTGTC-----GTTT--
seq0013        TTTAAGACTGCGTC-----GTTT-A
seq0014        TAGAAGACGTACGC-----GTCTAA
seq0015        TCGAA-ACTTCGTCTCCATGTCT-A
seq0018        -----------CTC-----GTCT-A
seq0020        TCTAAGACTTTGTC-----GTCT-A


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222
               0123456789012345678901234
                                        
seq0000        CCGAAGAG-TTTGTCATCT-----A
seq0001        CCGAAGAC-TTTGTCATCT-----A
seq0002        TCGAAGAC-TTTGTCATCT-----A
seq0003        TCGAAGAC-TTTGTCATCT-----A
seq0004        TCGAAGAC-TTTGTCATCT-----A
seq0005        TCGAAGAC-TTTGTCATCT-----A
seq0006        TCGAAGAC-TTTGTCATCT-----A
seq0007        TCGAAGAC-TTTGTCATCT-----A
seq0008        TAGACCAC-TTTTCGA-CT-----A
seq0009        TCGAAGAC-TTTGTCG-TT-----T
seq0013        TTTAAGAC-TGCGTCGTTT-----A
seq0014        TAGAAGACGTACGCGTCTA-----A
seq0015        TCGAA-AC-TTCGTCTCCATGTCTA
seq0018        ------------CTCGTCT-----A
seq0020        TCTAAGAC-TTTGTCGTCT-----A


<<<<< 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

seq0000   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0001   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0002   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0003   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0004   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0005   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0006   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0007   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0008   	    0    0    0    0    0    0    0    0    -    1    1    1    0    0   -5   -5    -   -4   -4    -    -    -    -    -    0
seq0009   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4    -   -3   -3    -    -    -    -    -    2
seq0013   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5    -    -    -    -    -    0
seq0015   	    0    0    0    0    0    -    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1   -4   -4   -4   -4    -    -    -    -    -    0
seq0020   	    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1   -4   -4   -4   -4    -    -    -    -    -    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	9	14	29	7	1	n/a	0,1,2,3,4,5,6,7,9,10,14
1	9	23	23	9	1	n/a	12
2	9	11	16	10	1	n/a	8
3	12	14	26	8	1	n/a	13
4	14	18	21	0	-5	n/a	11
5	14	18	16	1,4	-5,-4	0	8
6	15	18	29	2	-4	n/a	0,1,2,3,4,5,6,7,10,13,14
7	15	24	17	3,5,11	-4,-3,2	0,0	9



<<<<< 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	1	0	0	0	0	0
3	1	1	0	0	0	0
4	1	0	0	0	0	0
5	0	0	1	0	0	0
6	0	1	0	0	0	0
7	1	0	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	15	15	Shift(???)	23:14:18:-	23:19:23:-
2	0	3	3	Complex(???)	16:11:11:X	None
3	0	3	3	Shift(???)	26:0:10:X	26:0:11:X
4	0	5	5	Complex(???)	21:23:23:-	None
5	0	4	5	NO_ASSOCIATED_EVENT(???)	17:24:24:X	None
6	0	4	4	Complex(???)	None	18:16:16:X
7	0	4	10	Complex(???)	17:24:24:X	None


[ Contents of %indel_ref2assoc_cblks ]

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

26:0:10	3
23:5:5	{Equivalent to '23:5:5'(rec)}
16:11:11	2
23:14:18	1
21:23:23	4
17:24:24	5,7


[ Contents of %indel_rec2assoc_cblks ]

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

26:0:11	3
23:5:5	{Equivalent to '23:5:5'(ref)}
21:8:8	None
18:16:16	6
23:19:23	1


<<<< (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} = 0) ]

Indx_cblk_A	indx_cblk_B



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

