<<<<< 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 = 22 .


<< 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        C-GGCG--T--------------
seq0001        C-GGCG--T--------------
seq0002        C-GGCG--T--------------
seq0003        C-GGCG--T--------------
seq0004        C-GGCG--T--------------
seq0005        C-GGCG--TAGCTG--TTCCGTC
seq0006        C-GGCG--TAGCTG--TTCCGTC
seq0007        C-GGCG--TAGCTG--TTCAGTT
seq0008        C-GGCG--CACATG--ATCCGCC
seq0009        C-GGCG--CCGTTG--AGC-GCC
seq0013        CA---G--CAGAGG--CTCCGCT
seq0014        A-CGCG--CAGATGCCATCCGCC
seq0015        C-GGTG-CGAGATG--ACACGCA
seq0018        C-GCCGG-TAGCTG--ATCCGAC
seq0020        T-G-GG--CAGTTG--GTCCGC-


<< Original Segment of the Reconstructed Alignment: >>

(position)     0000000000111111111122
               0123456789012345678901
                                     
seq0000        CGGC-GT---------------
seq0001        CGGC-GT---------------
seq0002        CGGC-GT---------------
seq0003        CGGC-GT---------------
seq0004        CGGC-GT---------------
seq0005        CGGC-GT-AGCTGT--TCCGTC
seq0006        CGGC-GT-AGCTGT--TCCGTC
seq0007        CGGC-GT-AGCTGT--TCAGTT
seq0008        CGGC-GC-ACATGA--TCCGCC
seq0009        CGGC-GC-CGTTGA--GC-GCC
seq0013        --CA-GC-AGAGGC--TCCGCT
seq0014        ACGC-GC-AGATGCCATCCGCC
seq0015        CGGT-GCGAGATGA--CACGCA
seq0018        CGCCGGT-AGCTGA--TCCGAC
seq0020        TGG--GC-AGTTGG--TCCG-C


<<<<< 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

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




[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

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

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

0	1	1	29	10	1	n/a	0,1,2,3,4,5,6,7,8,9,11,12,13,14
1	2	2	28	4	0	n/a	14
2	3	4	20	12	3	n/a	10
3	3	3	28	2	-1	n/a	14
4	6	6	29	9	1	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,14
5	7	7	29	1	-1	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13,14
6	14	14	29	0	-2	n/a	5,6,7,8,9,10,12,13,14
7	22	22	28	11	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} = 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	1	0	0	0	0	0
2	2	1	0	0	0	0
3	1	1	0	0	0	0
4	1	1	0	0	0	0
5	1	1	0	0	0	0
6	1	1	0	0	0	0
7	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 0):  . ]


[ 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(???)	20:1:1:-	20:1:2:X
1	0	1	1	Complex(???)	27:3:3:-	None
2	0	2	2	Merge(complementary)(+shift^2)(?)	20:2:4:X/20:1:1:-	20:1:2:X
3	0	1	1	Shift	27:3:3:-	27:4:4:-
4	0	1	1	Shift	26:6:6:-	26:5:5:-
5	0	1	1	Shift	23:7:7:-	23:8:8:-
6	0	1	1	Shift	21:14:15:-	21:15:16:-
7	0	1	1	Shift	27:22:22:-	27:21:21:-


[ Contents of %indel_ref2assoc_cblks ]

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

20:1:1	0,2
20:2:4	2
27:3:3	1,3
26:6:6	4
23:7:7	5
9:9:22	{Equivalent to '9:9:22'(rec)}
21:14:15	6
17:19:19	{Equivalent to '17:19:19'(rec)}
27:22:22	7


[ Contents of %indel_rec2assoc_cblks ]

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

20:1:2	0,2
27:4:4	3
26:5:5	4
23:8:8	5
9:9:22	{Equivalent to '9:9:22'(ref)}
21:15:16	6
17:19:19	{Equivalent to '17:19:19'(ref)}
27:21:21	7


<<<< (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} = 0) ]

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



[ Contents of %cb2hard_linking (#{keys} = 0) ]

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



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

Indx_cblk_A	indx_cblk_B

2	0
3	1


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

[ For the 1 th pair: (2, 0) ]


{ The representative path is: 0  -> 2 }


( 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	0,1,2,3,4,5,6,7,8,9,11,12,13,14	0,1,2,3,4,5,6,7,8,9,11,12,13,14
2nd(reconstructed)	3	4	3	3	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)	Shift	20:1:1:-	20:0:0:-
2nd(reconstructed)	Merge(complementary)(+shift)(?)	20:2:4:X/20:0:0:-	20:1:2:X


[ For the 2 th pair: (3, 1) ]

