<<<<< 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 = 63 ,
#{Sites in the segment}_rec = 51 .


<< 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)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        A--------------------------------------------------CTC---ATG
seq0001        ------------------------------------------------------------
seq0002        A--------------------------------------------------CTC---ATG
seq0003        A--------------------------------------------------CTC---ATG
seq0004        A--------------------------------------------------CTC---ATG
seq0005        A--------------------------------------------------CTC---CTG
seq0006        G--------------------------------------------------CTC---ATG
seq0007        A--------------------------------------------------CTC---ATG
seq0008        G--------------------------------------------------CTC---ATG
seq0009        A--------------------------------------------------CAC---ATG
seq0013        A--------------------------------------------------CTC---AAG
seq0014        A--------------------------------------------------TTC---GTG
seq0015        A--------------------------------------------------CTCCTGATG
seq0018        A--------------------------------------------------CTC---GTG
seq0020        AAATCCTCGGGACATGTAGAGTGAACAGCTTAGGTATCCTTCAAATCCATA---------

(position)     666
               012
                  
seq0000        ATA
seq0001        --A
seq0002        TTA
seq0003        TTA
seq0004        TTA
seq0005        AT-
seq0006        AT-
seq0007        AT-
seq0008        ATA
seq0009        ATA
seq0013        ATA
seq0014        ATT
seq0015        ATA
seq0018        CTA
seq0020        ---


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445
               012345678901234567890123456789012345678901234567890
                                                                  
seq0000        ACTC-----------------------------------------ATGATA
seq0001        --------------------------------------------------A
seq0002        ACTC-----------------------------------------ATGTTA
seq0003        ACTC-----------------------------------------ATGTTA
seq0004        ACTC-----------------------------------------ATGTTA
seq0005        ACTC-----------------------------------------CTGAT-
seq0006        GCTC-----------------------------------------ATGAT-
seq0007        ACTC-----------------------------------------ATGAT-
seq0008        GCTC-----------------------------------------ATGATA
seq0009        ACAC-----------------------------------------ATGATA
seq0013        ACTC-----------------------------------------AAGATA
seq0014        ATTC-----------------------------------------GTGATT
seq0015        ACTCCTG--------------------------------------ATGATA
seq0018        ACTC-----------------------------------------GTGCTA
seq0020        AAATCCTCGGGACATGTAGAGTGAACAGCTTAGGTATCCTTCAAATCCATA


<<<<< 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, -12) .

[ 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   47   48   49

seq0000   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0003   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0004   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0005   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0006   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0007   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0008   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0009   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0013   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0014   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0015   	    0  -50  -50  -50  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
seq0018   	    0  -50  -50  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -12  -12  -12  -12  -12
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    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



(position)	   50

seq0000   	  -12
seq0001   	  -12
seq0002   	  -12
seq0003   	  -12
seq0004   	  -12
seq0005   	    -
seq0006   	    -
seq0007   	    -
seq0008   	  -12
seq0009   	  -12
seq0013   	  -12
seq0014   	  -12
seq0015   	  -12
seq0018   	  -12
seq0020   	    0




[INFORMATION] The original $commoner_shift_flank = -12. 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   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -   12  -38  -38  -38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62

seq0000   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0002   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0006   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0007   	    -    -    -    -    -    -    -    0    0    0    0    0    -
seq0008   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0020   	   12   12   12   12   12   12   12   12   12   12   12   12   12



<<<<< 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} = 4) >>

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

0	12	12	27	2	12	n/a	0,2,3,4,5,6,7,8,9,10,11,12,13
1	12	62	28	3	12	n/a	14
2	13	15	27	0	-38	n/a	0,2,3,4,5,6,7,8,9,10,11,13
3	13	18	23	1	-38	n/a	12



<<<<< 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} = 4) >>>>>


[[ 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	2	1	0	0	0	0
2
3	1	0	0	1	0	2


[ Skipped Composite-Blocks (#{cblocks} = 2): 0, 2 . ]


[ 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	51	51	Complex(???)	27:51:62:-/28:1:50:-	28:19:56:-
2	Skipped!!(NO_RELEVANT_BRANCH)
3	0	6	6	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	28:1:50:-/23:54:56:-	26:16:18:X/19:16:18:X/22:16:18:X


[ Contents of %indel_ref2assoc_cblks ]

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

2:0:61	{Equivalent to '2:12:61'(rec)}
28:1:50	1,3
27:51:62	1
23:54:56	3
14:62:62	{Equivalent to '14:62:62'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

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

2:12:61	{Equivalent to '2:0:61'(ref)}
26:16:18	3
22:16:18	3
19:16:18	3
28:19:56	1
14:62:62	{Equivalent to '14:62:62'(ref)}


<<<< (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]

0	=> [1],
2	=> [3],


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

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

1	=> [0],
3	=> [2],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 1) ]

Indx_cblk_A	indx_cblk_B

3	1


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

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


{ The representative path is: 3  -> 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)	13	18	-38	-38	23	0,2,3,4,5,6,7,8,9,10,11,12,13	12
2nd(reconstructed)	12	62	12	12	28	0,2,3,4,5,6,7,8,9,10,11,12,13,14	14


( 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)	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+2)(?)	28:1:50:-/23:54:56:-	26:16:18:X/19:16:18:X/22:16:18:X
2nd(reconstructed)	Complex(???)	28:19:50:-/28:1:12:-	28:19:56:-


