<<<<< 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 = 46 ,
#{Sites in the segment}_rec = 46 .


<< 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)     0000000000111111111122222222223333333333444444
               0123456789012345678901234567890123456789012345
                                                             
seq0000        TTGTACCATCATCTGCTTTGGTTTGAAGAA---GAATC--ACTCGG
seq0001        TTGTACTATCATCTGCTTTGGTTTGAAGAA---GAATC--ACTCGG
seq0002        TTGTACCATGATCTGCTTTGGTTTGAAGAA---GAATT--ACTCGG
seq0003        TTGTACCATGATCTGCTTTGGGTTGAAGAA---GAATT--ACTCTG
seq0004        TTGTACCATGATCTGCTTTGGTTTGAAG-------ATT--ACTCGG
seq0005        TGGTACCATGACCTGCTTGGGTTTGAAGAA---GAATT--ACTCGG
seq0006        TTGTACCATGACCTGCTTGGGTTTGAAGAA---GAATT--ACTCGG
seq0007        TTGTACCGCGACCCGCTTGGGTTTGAAGAA---GAATT--ACTCGG
seq0008        TTGTACCACGATCTGCTTAGGCTTGAACTA---GACTT--ACTC--
seq0009        TTGTACCACGATCTGCTTAGGCTTGAACAA---AAATT---CTTGG
seq0013        T--------GACCTGCTTGGGGTTGACGAA---CAATTGCACGCTG
seq0014        TTGTCCCACGA-GAGCTTGGG---GGAGAA---CAATT--ACTCGG
seq0015        TTGTCCCACGATCTGCTTTTGCTTGAAGAA---CAATC--ACTCGG
seq0018        ATCTACCACGATCTGCTTTCGCTTCAGGAAACGGCAAG--------
seq0020        TTGTACAACTATCTGTTTTAGCTTGAGGAA---GAATG---CTC-C


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333444444
               0123456789012345678901234567890123456789012345
                                                             
seq0000        TTGTACCATCATCTGCTTTGGTTTGAAG---AAGAATC--ACTCGG
seq0001        TTGTACTATCATCTGCTTTGGTTTGAAG---AAGAATC--ACTCGG
seq0002        TTGTACCATGATCTGCTTTGGTTTGAAG---AAGAATT--ACTCGG
seq0003        TTGTACCATGATCTGCTTTGGGTTGAAG---AAGAATT--ACTCTG
seq0004        TTGTACCATGATCTGCTTTGGTTTGAAG-------ATT--ACTCGG
seq0005        TGGTACCATGACCTGCTTGGGTTTGAAG---AAGAATT--ACTCGG
seq0006        TTGTACCATGACCTGCTTGGGTTTGAAG---AAGAATT--ACTCGG
seq0007        TTGTACCGCGACCCGCTTGGGTTTGAAG---AAGAATT--ACTCGG
seq0008        TTGTACCACGATCTGCTTAGGCTTGAAC---TAGACTT--ACTC--
seq0009        TTGTACCACGATCTGCTTAGGCTTGAAC---AAAAATT--CTTG-G
seq0013        -TGACCTGCTTG-------GGGTTGACG---AACAATTGCACGCTG
seq0014        TTGTCCCACGAG-------AGCTTGGGGGAGAACAATT--ACTCGG
seq0015        TTGTCCCACGATCTGCTTTTGCTTGAAG---AACAATC--ACTCGG
seq0018        ATCTACCACGATCTGCTTTCGCTTCAGG---AAACGGC--A---AG
seq0020        TTGTACAACTATCTGTTTTAGCTTGAGG---AAGAATG---CTCC-


<<<<< 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

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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    -    -    -    -    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    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    0    0    0    0    -    -    -    3    3    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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -   -1   -1   -1   -1    -    0
seq0013   	    -    1   -7   -7   -7   -7   -7   -7   -7   -7   -7   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3    3    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0   -1    -    -    -    -    -    -    -    6    6    6    6    6    6    6    6    3    3    3    3    3    3    0    0    0    0    0    -    -    0    0    0    0    0    0
seq0015   	    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    -    -    -    3    3    0    0    0    0    0    -    -    0    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    -    -    -    3    3    3    3    3    3    3    -    -    5    -    -    -    8    8
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    0    0    0    0    -    -    -    3    3    0    0    0    0    0    -    -    -    0    0    0   -1    -



<<<<< 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	1	1	20	7	1	n/a	10
1	2	11	20	0	-7	n/a	10
2	11	26	21	2,12	-1,6	0	11
3	27	32	21	10	3	n/a	11
4	31	32	29	8	3	n/a	0,1,2,3,5,6,7,8,9,10,12,14
5	31	40	26	9,11	3,5	0	13
6	40	43	17	3	-1	n/a	9
7	44	45	26	13	8	n/a	13
8	44	44	28	1	-1	n/a	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	0	0	1	0	0
2	2	0	0	0	0	0
3	1	1	0	0	0	0
4
5	1	1	0	1	0	0
6	1	0	0	1	0	0
7	0	1	1	1	0	0
8	0	1	2	1	0	0


[ Skipped Composite-Blocks (#{cblocks} = 1): 4 . ]


[ 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(???)	20:1:8:X	20:0:0:X
1	0	10	10	Complex(???)	20:1:8:X	22:12:18:X
2	0	9	16	Complex(???)	21:11:11:X/21:21:23:X	None
3	0	6	6	Complex(???)	21:21:23:X	21:28:30:-
4	Skipped!!(NO_RELEVANT_BRANCH)
5	0	8	10	Complex(???)	26:30:32:-	26:41:43:X/27:40:40:-
6	0	4	4	Complex(???)	17:40:40:X	18:44:44:X
7	0	2	2	Complex(???)	25:40:40:-	26:41:43:X/27:45:45:-
8	0	1	1	Complex(???)	25:44:44:-/26:41:45:X	27:45:45:-/26:41:43:X


[ Contents of %indel_ref2assoc_cblks ]

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

20:1:8	0,1
21:11:11	2
21:21:23	2,3
6:28:34	{Equivalent to '6:31:34'(rec)}
26:30:32	5
20:38:39	{Equivalent to '20:38:39'(rec)}
25:40:40	7
17:40:40	6
26:41:45	8
25:44:44	8
16:44:45	None


[ Contents of %indel_rec2assoc_cblks ]

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

20:0:0	0
22:12:18	1
21:28:30	3
6:31:34	{Equivalent to '6:28:34'(ref)}
20:38:39	{Equivalent to '20:38:39'(ref)}
27:40:40	5
26:41:43	5,7,8
18:44:44	6
27:45:45	7,8
16:45:45	None


<<<< (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]

4	=> [3,5],


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

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

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


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

Indx_cblk_A	indx_cblk_B

0	1
2	3


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

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


{ The representative path is: 0  -> 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)	1	1	1	1	20	10	10
2nd(reconstructed)	2	11	-7	-7	20	10	10


( 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)	Split(same-type)	20:1:8:X	20:0:0:X/20:2:8:X
2nd(reconstructed)	Neighboring-branch-Merge(2del)(?)	20:2:8:X/21:12:18:X	22:12:18:X


[ For the 2 th pair: (2, 3) ]

