<<<<< 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 = 42 ,
#{Sites in the segment}_rec = 41 .


<< 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)     000000000011111111112222222222333333333344
               012345678901234567890123456789012345678901
                                                         
seq0000        -----------------CTGATGGTGGTTTGCCCAAT-CCA-
seq0001        -----------------CTTATGGTGGTTTGCCCAAT-CCA-
seq0002        -----------------TTGATGGTGGTTCGACCA-T-CCA-
seq0003        -----------------TTGATGGTGGTTCGACCA-T-CCA-
seq0004        -----------------TTGATGGTGGTTC---CA-T-CCA-
seq0005        -----------------CTGATGGTGGTTCGACCAAT-CCA-
seq0006        -----------------CTGATGGTGGTTCGACAAAC-CCA-
seq0007        -----------------CTGATGGTGGTTCGACCAAT-CCA-
seq0008        -----------------CTAATGGTAGTTCGACCAAT-CCA-
seq0009        -----------------CTAATGGGAGTTCGACCAATCCCA-
seq0013        -----------------ATAATGGTTGCTCGACCAAT-CCA-
seq0014        -----------------GAAAGGG-----CGACCAAT-CCA-
seq0015        GCTAACCATGACCGCGTAGAATGGCAGTTCGCCCAAT-TCA-
seq0018        -----------------CTAATGGCGG-TCAACCAAT-ACAA
seq0020        -----------------CT-----------------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     00000000001111111111222222222233333333334
               01234567890123456789012345678901234567890
                                                        
seq0000        -----------------CTGATGGTGGTTTGCCCAAT-CCA
seq0001        -----------------CTTATGGTGGTTTGCCCAAT-CCA
seq0002        -----------------TTGATGGTGGTTCGACC-AT-CCA
seq0003        -----------------TTGATGGTGGTTCGACC-AT-CCA
seq0004        -----------------TTGATGGTGGTT---CC-AT-CCA
seq0005        -----------------CTGATGGTGGTTCGACCAAT-CCA
seq0006        -----------------CTGATGGTGGTTCGACAAAC-CCA
seq0007        -----------------CTGATGGTGGTTCGACCAAT-CCA
seq0008        -----------------CTAATGGTAGTTCGACCAAT-CCA
seq0009        -----------------CTAATGGGAGTTCGACCAATCCCA
seq0013        -----------------ATAATGGTTGCTCGACCAAT-CCA
seq0014        -----------------GAAAGGG-----CGACCAAT-CCA
seq0015        GCTAACCATGACCGCGTAGAATGGCAGTTCGCCCAAT-TCA
seq0018        -----------------CTAATGGCGGTCAACCAATA-CAA
seq0020        ---------------------------------------CT


<<<<< 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

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    -    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    -    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    0    -    1    0    -    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0
seq0015   	    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
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2    -   -1   -1   -1
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   22   22



<<<<< 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	27	40	26	1,0,2	-1,-2,-1	0,0	13
1	32	32	6	5	3	n/a	4
2	35	35	8	4	1	n/a	2,3,4
3	39	40	28	6	22	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} = 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	0	1	0	0	0
1	1	1	0	0	0	0
2	1	1	0	0	0	0
3	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	14	14	Complex(???)	26:41:41:-/25:27:27:-	None
1	0	1	1	Shift	6:30:32:X	6:29:31:X
2	0	1	1	Shift	8:35:35:X	8:34:34:X
3	0	2	2	Complex(???)	27:19:40:-	27:17:38:-


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:16	{Equivalent to '23:0:16'(rec)}
27:19:40	3
21:24:28	{Equivalent to '21:24:28'(rec)}
25:27:27	0
6:30:32	1
8:35:35	2
17:37:37	{Equivalent to '17:37:37'(rec)}
26:41:41	0


[ Contents of %indel_rec2assoc_cblks ]

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

23:0:16	{Equivalent to '23:0:16'(ref)}
27:17:38	3
21:24:28	{Equivalent to '21:24:28'(ref)}
6:29:31	1
8:34:34	2
17:37:37	{Equivalent to '17:37:37'(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} = 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} = 0) ]

Indx_cblk_A	indx_cblk_B



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

