<<<<< 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 = 34 ,
#{Sites in the segment}_rec = 29 .


<< 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)     0000000000111111111122222222223333
               0123456789012345678901234567890123
                                                 
seq0000        ----TG-ACTC---AAA-ATTAAAAG-------A
seq0001        ----TG-ACTC---AAA-ATTAAAAG-------A
seq0002        ----TT-ATTC---AAA-ATTAAAAG-------A
seq0003        ----TT-ACTC---AAA-ATTAAAAG-------A
seq0004        ----TT-ACTC---AAA-ATTAAAAG-------A
seq0005        ----TG-ACTC---AAA-ATTAAAAG-------A
seq0006        ----TG-TCTC---AAA-ATTAAAAG-------A
seq0007        ----TG-ACTC---AAA-ATTAAAAG-------A
seq0008        ----GC-ACTC---ATG-ATGGACAG-------C
seq0009        ----GG-ACTC---AAG-ATGTACTG-------A
seq0013        ---GTG-T--CTCT--T-CTGTGCAGCTTCACAG
seq0014        ----TG-ACTC---AAA-ATATGAAC-------A
seq0015        ----TG-ACTC---AAATATTTGATG-------A
seq0018        CTA-TT-CGTT---AAA-ATGTTAAG-------A
seq0020        ----TGAAGTA---AAA-TTGTTAAG-------A


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222
               01234567890123456789012345678
                                            
seq0000        -TGACTC---AAA------ATTAAAAGA-
seq0001        -TGACTC---AAA------ATTAAAAGA-
seq0002        -TTATTC---AAA------ATTAAAAGA-
seq0003        -TTACTC---AAA------ATTAAAAGA-
seq0004        -TTACTC---AAA------ATTAAAAGA-
seq0005        -TGACTC---AAA------ATTAAAAGA-
seq0006        -TGTCTC---AAA------ATTAAAAGA-
seq0007        -TGACTC---AAA------ATTAAAAGA-
seq0008        -GCACTC---ATG------ATGGACAGC-
seq0009        -GGACTC---AAG------ATGTACTGA-
seq0013        GTGTCTC---TTC-TGTGCAGCTTCACAG
seq0014        -TGACTC---AAA------ATATGAACA-
seq0015        -TGACTC---AAAT-----ATTTGATGA-
seq0018        -CTATTCGTTAAA------ATGTTAAGA-
seq0020        -TGAA--GTAAAA------TTGTTAAGA-


<<<<< 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, -5) .

[ 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

seq0000   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0001   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0002   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0003   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0004   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0005   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0006   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0007   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0008   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0009   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0013   	   -3   -3   -3   -4   -6   -6   -6    -    -    -   -3   -5   -6    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0014   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0015   	    -   -3   -3   -4   -4   -4   -4    -    -    -   -4   -4   -4   -4    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0018   	    -    1    1    1    0    0   -1   -1   -1   -1   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -
seq0020   	    -   -3   -3   -3   -3    -    -   -1   -1   -1   -4   -4   -4    -    -    -    -    -    -    1    1    1    1    1    1    1    1   -6    -




[INFORMATION] The original $commoner_shift_flank = -5. Thus, we will shift the entire reconstructed MSA ...

<< REVISED Output of 'map_shifts_respos_bw_2msas' >>

New ($shift_lf, $shift_rf) = (0, 0) .

[ New 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

seq0000   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0001   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0002   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0003   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0004   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0005   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0006   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0007   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0008   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0009   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0013   	    -    -    -    -    -    2    2    2    1   -1   -1   -1    -    -    -    2    0   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0015   	    -    -    -    -    -    -    2    2    1    1    1    1    -    -    -    1    1    1    1    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0018   	    -    -    -    -    -    -    6    6    6    5    5    4    4    4    4    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -1    -
seq0020   	    -    -    -    -    -    -    2    2    2    2    -    -    4    4    4    1    1    1    -    -    -    -    -    -    6    6    6    6    6    6    6    6   -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} = 12) >>

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

0	5	8	20	10,7	2,1	0	10
1	6	7	25	9	2	n/a	0,1,2,3,4,5,6,7,8,9,11,12
2	6	14	26	16,14,13	6,5,4	0,0	13
3	6	9	28	8	2	n/a	14
4	8	17	25	5	1	n/a	0,1,2,3,4,5,6,7,8,9,11
5	8	18	23	6	1	n/a	12
6	9	15	20	1,11	-1,2	0	10
7	12	14	28	12	4	n/a	14
8	15	17	29	4	1	n/a	13,14
9	16	17	20	3,2	0,-1	0	10
10	24	31	29	15	6	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13,14
11	32	32	29	0	-1	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13,14



<<<<< 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} = 12) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 2): 4, 5 . ]


[ 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	5	4	Complex(???)	20:8:9:X	None
1	0	2	2	NO_ASSOCIATED_EVENT(???)	28:6:6:-	None
2	0	11	9	Complex(???)	26:0:2:-	25:12:14:X
3	0	4	4	Complex(???)	28:6:6:-/26:0:2:-	27:10:11:-
4	Skipped!!(NO_RELEVANT_BRANCH)
5	Skipped!!(NO_ASSOCIATED_EVENT(???))
6	0	4	7	Complex	20:8:9:X/20:14:15:X/20:11:13:-	None
7	0	3	3	Complex(???)	None	27:10:11:-/25:12:14:X
8	0	3	3	Complex(???)	None	25:12:14:X
9	0	3	2	Complex(???)	20:14:15:X	20:19:23:-
10	0	8	8	Complex(???)	20:26:32:-	20:19:23:-
11	0	1	1	Complex(???)	20:26:32:-	20:33:33:-


[ Contents of %indel_ref2assoc_cblks ]

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

26:0:2	2,3
20:3:3	{Equivalent to '20:5:5'(rec)}
28:6:6	1,3
20:8:9	0,6
20:11:13	6
20:14:15	6,9
23:17:17	{Equivalent to '23:18:18'(rec)}
20:26:32	10,11


[ Contents of %indel_rec2assoc_cblks ]

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

20:5:5	{Equivalent to '20:3:3'(ref)}
27:10:11	3,7
25:12:14	2,7,8
23:18:18	{Equivalent to '23:17:17'(ref)}
20:19:23	9,10
20:33:33	11


<<<< (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]

1	=> [3],


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

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

3	=> [1],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

