<<<<< 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 = 47 ,
#{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)     00000000001111111111222222222233333333334444444
               01234567890123456789012345678901234567890123456
                                                              
seq0000        CAC--------G-----------------------------CAGCGT
seq0001        CAC--------G-----------------------------CAGCGT
seq0002        CA---------------------------------------CAGCGT
seq0003        CA---------------------------------------CAACGT
seq0004        CA---------------------------------------CAGCGT
seq0005        GAT--------G-----------------------------CAGCAT
seq0006        CAT--------G-----------------------------CAGCAT
seq0007        CAT--------G-----------------------------CAGCAT
seq0008        CAT--------C-----------------------------CAACAA
seq0009        CATAGAAGAACG-----------------------------CACAAG
seq0013        CAT--------G-----------------------------CAAC-T
seq0014        -AA--------GGTTTGGGCGACCATTACACCTGTTCCCTGCAACAT
seq0015        TAA--------G-----------------------------CTA--T
seq0018        CAA--------G-----------------------------CAACAT
seq0020        CAT--------G-----------------------------CAACAT


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122222222223333333333444444
               0123456789012345678901234567890123456789012345
                                                             
seq0000        ----------------------------CACGCAGCGT--------
seq0001        ----------------------------CACGCAGCGT--------
seq0002        ----------------------------CAC--AGCGT--------
seq0003        ----------------------------CAC--AACGT--------
seq0004        ----------------------------CAC--AGCGT--------
seq0005        ----------------------------GATGCAGCAT--------
seq0006        ----------------------------CATGCAGCAT--------
seq0007        ----------------------------CATGCAGCAT--------
seq0008        ----------------------------CATCCAACAA--------
seq0009        ----------------------------CATAGAAGAACGCACAAG
seq0013        ----------------------------CATGCAAC-T--------
seq0014        AAGGTTTGGGCGACCATTACACCTGTTCCCTGCAACAT--------
seq0015        ----------------------------TAAGCTA--T--------
seq0018        ----------------------------CAAGCAACAT--------
seq0020        ----------------------------CATGCAACAT--------


<<<<< 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, -1) .

[ 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28  -11    -    -   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28  -11    -    -   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28  -11    -    -   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   28   28   28   28   28   28   28   28   28   -1   -1   -1   -1   -1   -1
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9    -   -9    -    -    -    -    -    -    -    -
seq0014   	   -1   -1   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9    -    -   -9    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   28   28   28   20   -9   -9   -9   -9   -9   -9    -    -    -    -    -    -    -    -




[INFORMATION] The original $commoner_shift_flank = -1. 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   34   35   36   37   38   39   40   41   42   43   44   45   46

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29  -10    -    -   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29  -10    -    -   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29  -10    -    -   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   29   29   29   29   29   29   29   29   29    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8    -   -8    -    -    -    -    -    -    -    -
seq0014   	    -    0    0   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8    -    -   -8    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   29   29   29   21   -8   -8   -8   -8   -8   -8    -    -    -    -    -    -    -    -



<<<<< 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	3	38	21	2	-8	n/a	11
1	29	31	29	5	29	n/a	0,1,5,6,7,8,10,12,13,14
2	29	30	8	7	29	n/a	2,3,4
3	29	40	17	6	29	n/a	9
4	31	31	8	0	-10	n/a	2,3,4
5	32	32	29	4	21	n/a	0,1,5,6,7,8,10,12,13,14
6	33	38	29	1	-8	n/a	0,1,5,6,7,8,10,12,13,14
7	34	38	8	3	-8	n/a	2,3,4



<<<<< 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	0	0	0	0
1
2	1	0	0	0	0	0
3	1	1	0	0	0	0
4	1	1	0	0	0	0
5
6
7	0	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 1, 5, 6 . ]


[ 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	36	36	Complex(???)	21:12:40:-	21:1:28:-
1	Skipped!!(NO_RELEVANT_BRANCH)
2	0	2	2	Complex(???)	8:2:11:X	None
3	0	12	12	Shift(???)	17:3:10:-	17:39:46:-
4	0	1	1	Shift	8:2:11:X	8:32:33:X
5	Skipped!!(NO_RELEVANT_BRANCH)
6	Skipped!!(NO_RELEVANT_BRANCH)
7	0	5	5	Complex(???)	None	8:32:33:X


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:0	None
8:2:11	2,4
17:3:10	3
21:12:40	0
23:44:45	None
20:45:45	{Equivalent to '20:37:37'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

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

21:1:28	0
8:32:33	4,7
23:36:37	None
20:37:37	{Equivalent to '20:45:45'(ref)}
17:39:46	3


<<<< (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	=> [3],
6	=> [0],


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

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

0	=> [6],
3	=> [1],


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

Indx_cblk_A	indx_cblk_B

4	7
4	2


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

[ For the 1 th pair: (4, 7) ]


{ The representative path is: 4  -> 7 }


( 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)	31	31	-10	-10	8	2,3,4	2,3,4
2nd(reconstructed)	34	38	-8	-8	8	2,3,4	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(???)	8:2:11:X	8:32:38:X
2nd(reconstructed)	Complex(???)	8:32:38:X/3:42:46:X	8:32:33:X


[ For the 2 th pair: (4, 2) ]

