<<<<< 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 = 23 ,
#{Sites in the segment}_rec = 20 .


<< 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)     00000000001111111111222
               01234567890123456789012
                                      
seq0000        -A-AGC-AATATTTCCG---GG-
seq0001        -A-AGC-AATATTTCCG---GG-
seq0002        -A-CGC-AATATTTCCGC-TGG-
seq0003        -G-CGC-AATATTTCCGC-TGG-
seq0004        -A-CGC-AATATTTCCGC-TGG-
seq0005        -A-CGCTAATATT-CCGC-CGG-
seq0006        -A-CGCTAATATT-C------G-
seq0007        -T-CGCTAATATT-CCGC-TGG-
seq0008        -A-AGCTTATATTTGCGC-TAGA
seq0009        AA-AGCTAAGCTTTCCGG-TGG-
seq0013        -A-ACTTTTTATTTCCGC-TGC-
seq0014        -A-GTTTTATAATTCGGC-TGG-
seq0015        -A-AGCTTATAGTTCCGC-TGC-
seq0018        -AAAGTCAGTATTTCCGC-TGC-
seq0020        -G-AGTCAATACTTCCTGCTGT-


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111
               01234567890123456789
                                   
seq0000        AAGC--AATATTTCCG--GG
seq0001        AAGC--AATATTTCCG--GG
seq0002        ACGC--AATATTTCCGCTGG
seq0003        GCGC--AATATTTCCGCTGG
seq0004        ACGC--AATATTTCCGCTGG
seq0005        ACGC--TAATATTCCGCCGG
seq0006        ACGC--TAATATTC-----G
seq0007        TCGC--TAATATTCCGCTGG
seq0008        AAGCTTATATTTGCGCTAGA
seq0009        AAAGCTAAGCTTTCCGGTGG
seq0013        AACTT-TTTATTTCCGCTGC
seq0014        AGTTT-TATAATTCGGCTGG
seq0015        AAGCT-TATAGTTCCGCTGC
seq0018        AAAGTCAGTATTTCCGCTGC
seq0020        GAGTCAATACTTCCTGCTGT


<<<<< 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, -3) .

[ 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

seq0000   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2
seq0001   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2
seq0002   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0003   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0004   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0005   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1   -2   -2   -2
seq0006   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1    -    -    -    -    -   -2
seq0007   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1   -2   -2   -2
seq0008   	   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3
seq0009   	    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0013   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0014   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0015   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0020   	   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2



<<<<< 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} = 15) >>

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

0	0	0	29	8	-1	n/a	0,1,2,3,4,5,6,7,8,10,11,12,14
1	0	16	26	10	-1	n/a	13
2	1	3	15	4	-2	n/a	0,1,2,3,4,5,6,7
3	1	4	24	3	-2	n/a	10,11,12
4	1	19	28	2	-2	n/a	14
5	1	19	16	5,0	-2,-3	0	8
6	2	16	17	11	-1	n/a	9
7	6	15	3	13	-1	n/a	0,1
8	6	16	25	9	-1	n/a	2,3,4,10,11,12
9	6	12	14	15	0	n/a	5,6,7
10	13	16	14	12	-1	n/a	5,7
11	13	13	11	14	-1	n/a	6
12	17	19	27	1	-2	n/a	2,3,4,5,7,9,10,11,12,13
13	18	19	3	6	-2	n/a	0,1
14	19	19	11	7	-2	n/a	6



<<<<< 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} = 15) >>>>>


[[ 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	0	0	0
1	1	0	1	0	0	0
2	0	1	1	0	0	0
3	0	1	0	0	0	0
4	1	0	1	0	0	0
5	1	0	0	0	0	0
6	0	0	0	0	0	0
7	0	0	1	0	0	0
8
9	1	0	1	1	0	0
10	1	0	0	0	0	0
11	0	0	0	0	0	0
12
13	0	0	0	0	0	0
14	0	0	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 6): 6, 8, 11, 12, 13, 14 . ]


[ 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(???)	17:0:0:-	None
1	0	17	17	Complex(???)	26:2:2:-/28:18:18:-	None
2	0	3	3	Complex(???)	9:6:6:X	15:4:5:X
3	0	4	4	Complex(???)	None	24:5:5:X
4	0	19	19	Complex(???)	28:18:18:-/26:2:2:-	None
5	0	20	19	Complex(???)	16:22:22:-	None
6	Skipped!!(NO_ASSOCIATED_EVENT(???))
7	0	10	10	NO_ASSOCIATED_EVENT(???)	9:6:6:X	None
8	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
9	0	7	7	Complex(???)	14:13:13:X/9:6:6:X	15:4:5:X
10	0	4	4	Complex(???)	14:13:13:X	None
11	Skipped!!(NO_ASSOCIATED_EVENT(???))
12	Skipped!!(NO_RELEVANT_BRANCH)
13	Skipped!!(NO_ASSOCIATED_EVENT(???))
14	Skipped!!(NO_ASSOCIATED_EVENT(???))


[ Contents of %indel_ref2assoc_cblks ]

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

17:0:0	0
26:2:2	1,4
9:6:6	2,7,9
14:13:13	9,10
11:15:20	{Equivalent to '11:14:18'(rec)}
3:17:19	{Equivalent to '3:16:17'(rec)}
28:18:18	1,4
16:22:22	5


[ Contents of %indel_rec2assoc_cblks ]

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

15:4:5	2,9
24:5:5	3
11:14:18	{Equivalent to '11:15:20'(ref)}
3:16:17	{Equivalent to '3:17:19'(ref)}


<<<< (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} = 3) ]

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

8	=> [1],
11	=> [10],
12	=> [4],


[ Contents of %cb2hard_linking (#{keys} = 3) ]

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

1	=> [8],
4	=> [12],
10	=> [11],


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

Indx_cblk_A	indx_cblk_B

1	4


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

[ For the 1 th pair: (1, 4) ]


{ The representative path is: 1  -> 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)	0	16	-1	-1	26	13	2,3,4,10,11,12,13
2nd(reconstructed)	1	19	-2	-2	28	14	2,3,4,5,7,9,10,11,12,13,14


( 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)	Complex(???)	26:2:2:-/28:18:18:-	26:17:18:X
2nd(reconstructed)	Complex(???)	27:1:2:-	None


