<<<<< 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 = 40 .


<< 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        GGCCGTA--------AGGTAGAATCTA-CGT--ATTA---T--
seq0001        GGCCGTA--------AGGTAGAATCTA-CGT--ATTA---T--
seq0002        -----------------GTAGCATCGA-CGT--ATTA---T--
seq0003        -----------------CTAGCATCGA-CGT--ATTA---T--
seq0004        -----------------CTAGCATCGA-CGT--ATTA---T--
seq0005        GGCCG-----------G-TAGTATCGA-CGT--ATTG---T--
seq0006        GGCCGTA--------AG-TAGTATCGA-CGT--ATTG---TCT
seq0007        GGACGTA--------AG-TCGTATCGA-CGT--ATTG---T--
seq0008        GCCCGTA--------AG-TAGTATAT---GT--ATTA---T--
seq0009        GCCCGTA--------AG-TAGTATAG---GT--ATTA---G--
seq0013        GACCGTA--------AG-TA-TATCGA-TCTCCATTC---T--
seq0014        GTCCATA--------TG-TTGTATCGAACGT--ATTT---T--
seq0015        CACCGTA--------CG-TAGCATCGA-CGT--ATTG---T--
seq0018        GGCCGTA--------GG-AAGTATCGA-CGG--ATGT---T--
seq0020        AGCCGTAATGCCAACTG-TACTATCGT-CGT--CCTGTCGT--


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333
               0123456789012345678901234567890123456789
                                                       
seq0000        GGCCGTAAG----------GTAGAATCT-ACGTATTA--T
seq0001        GGCCGTAAG----------GTAGAATCT-ACGTATTA--T
seq0002        -------------------GTAGCATCG-ACGTATTA--T
seq0003        -------------------CTAGCATCG-ACGTATTA--T
seq0004        -------------------CTAGCATCG-ACGTATTA--T
seq0005        GGCCG--------------GTAGTATCG-ACGTATTG--T
seq0006        GGCCGTAA-----------GTAGTATCG-ACGTATTGTCT
seq0007        GGACGTAA-----------GTCGTATCG-ACGTATTG--T
seq0008        GCCCGTAA-----------GTAGTAT---ATGTATTA--T
seq0009        GCCCGTAA-----------GTAGTAT---AGGTATTA--G
seq0013        GACCGTAA-----------GTATATCGATCTCCATTC--T
seq0014        GTCCATAT-----------GTTGTATCGAACGTATTT--T
seq0015        CACCGTAC-----------GTAGCATCG-ACGTATTG--T
seq0018        GGCCGTAG-----------GAAGTATCG-ACGGATGT--T
seq0020        AGCCGTAATGCCAACTGTACTATCGTCG-TCCTGTCG--T


<<<<< 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   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39

seq0000   	    0    0    0    0    0    0    0   -8   -8    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0001   	    0    0    0    0    0    0    0   -8   -8    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0005   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0006   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0   -3   -3   -3
seq0007   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0008   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    -    -    -    5    5    2    2    0    0    0    0    -    -   -1
seq0009   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    -    -    -    5    5    2    2    0    0    0    0    -    -   -1
seq0013   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    -    -   -1
seq0014   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    2    2    2    2    2    0    0    0    0    -    -   -1
seq0015   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0018   	    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    -    -    -    3    2    2    2    2    2    2    2    2    -    3    2    2    2    0    0    0    0    -    -   -1
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2    -   -1   -3   -3   -3   -3   -3   -3   -3    -    -   -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} = 16) >>

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

0	7	8	3	1	-8	n/a	0,1
1	7	7	27	0	-8	n/a	6,7,8,9,10,11,12,13
2	17	36	28	6,4,7,2	-1,-2,-1,-3	0,0,0	14
3	19	27	9	16	2	n/a	0,1,2,3,4
4	19	19	27	19	3	n/a	5,6,7,8,9,10,11,12,13
5	20	21	20	17	2	n/a	10
6	20	32	21	15	2	n/a	11
7	20	27	27	12	2	n/a	5,6,7,12,13
8	20	25	18	13	2	n/a	8,9
9	22	36	20	10,9	1,0	0	10
10	29	32	27	18,11	3,2	0	0,1,2,3,4,5,6,7,12,13
11	29	30	18	20	5	n/a	8,9
12	31	32	18	14	2	n/a	8,9
13	33	36	27	8	0	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13
14	37	39	11	3	-3	n/a	6
15	39	39	29	5	-1	n/a	0,1,2,3,4,5,7,8,9,10,11,12,13,14



<<<<< 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} = 16) >>>>>


[[ 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	0	0	2	1	0	0
1
2	1	1	0	0	0	0
3	1	0	1	2	0	0
4
5	1	0	0	0	0	0
6	1	0	1	0	0	0
7	0	1	0	0	0	0
8	0	1	0	0	0	0
9	2	0	0	0	0	0
10	0	1	1	0	0	0
11	1	1	0	0	0	0
12	1	0	0	0	0	0
13
14	1	1	0	0	0	0
15	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 1, 4, 13 . ]


[ 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	2	2	Complex	9:17:17:-/8:0:16:X	8:0:8:X
1	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
2	0	22	20	Complex(???)	28:37:39:-	28:9:18:-
3	0	9	9	Complex(???)	9:17:17:-/8:0:16:X	14:8:8:X/8:0:8:X
4	Skipped!!(NO_RELEVANT_BRANCH)
5	0	2	2	Complex(???)	20:20:20:X	None
6	0	13	13	Complex(???)	21:27:27:-/20:31:32:-	None
7	0	8	8	Complex(???)	None	22:28:28:-
8	0	6	6	Complex(???)	None	18:26:27:X
9	0	16	15	Complex(???)	20:20:20:X/20:31:32:-	None
10	0	5	4	Complex(???)	20:31:32:-	22:28:28:-
11	0	2	2	Shift	18:26:28:X	18:26:27:X
12	0	2	2	Complex(???)	18:26:28:X	None
13	Skipped!!(NO_RELEVANT_BRANCH)
14	0	3	3	Shift(?)	11:41:42:-	11:37:38:-
15	0	1	1	Shift	11:41:42:-	11:37:38:-


[ Contents of %indel_ref2assoc_cblks ]

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

8:0:16	0,3
10:5:15	{Equivalent to '10:5:7'(rec)}
28:7:14	None
9:17:17	0,3
20:20:20	5,9
18:26:28	11,12
21:27:27	6
20:31:32	6,9,10
28:37:39	2
11:41:42	14,15


[ Contents of %indel_rec2assoc_cblks ]

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

8:0:8	0,3
10:5:7	{Equivalent to '10:5:15'(ref)}
26:8:8	None
24:8:8	None
18:8:8	None
14:8:8	3
28:9:18	2
18:26:27	8,11
22:28:28	7,10
11:37:38	14,15


<<<< (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} = 2) ]

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

1	=> [0],
13	=> [9],


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

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

0	=> [1],
9	=> [13],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 3) ]

Indx_cblk_A	indx_cblk_B

0	3
11	12
11	8


[[ 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)	7	8	-8	-8	3	0,1,6,7,8,9,10,11,12,13	0,1
2nd(reconstructed)	19	27	2	2	9	0,1,2,3,4	0,1,2,3,4


( 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	9:17:17:-/8:0:16:X	8:0:8:X
2nd(reconstructed)	Complex(???)	9:26:27:X	14:8:8:X


[ For the 2 th pair: (11, 12) ]

[ For the 3 th pair: (11, 8) ]

