<<<<< 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 = 67 ,
#{Sites in the segment}_rec = 54 .


<< 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        G-------------------------------------------------CAA-------
seq0001        G-------------------------------------------------CAA-------
seq0002        G-------------------------------------------------CAA-------
seq0003        GCGCATACCGTAAGGGACACCGAACGCCCAGCCCGAACCAAAGGCCGGGGCAA-------
seq0004        G-------------------------------------------------CAA-------
seq0005        G-------------------------------------------------CAA-------
seq0006        G-------------------------------------------------CAA-------
seq0007        G-------------------------------------------------CAA-------
seq0008        A-------------------------------------------------CAC-------
seq0009        A-------------------------------------------------CAA-------
seq0013        A-------------------------------------------------CAT-------
seq0014        A-------------------------------------------------CTT-------
seq0015        C-------------------------------------------------CATCGTCTCC
seq0018        T-------------------------------------------------CAA-------
seq0020        --------------------------------------------------CAT-------

(position)     6666666
               0123456
                      
seq0000        -----G-
seq0001        -----G-
seq0002        -----G-
seq0003        -----G-
seq0004        -----G-
seq0005        -----G-
seq0006        -----G-
seq0007        -----G-
seq0008        -----G-
seq0009        -----G-
seq0013        -----T-
seq0014        -----G-
seq0015        ACGCCG-
seq0018        -----G-
seq0020        -----GA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555
               012345678901234567890123456789012345678901234567890123
                                                                     
seq0000        -------------------------------------------------GCAAG
seq0001        -------------------------------------------------GCAAG
seq0002        -------------------------------------------------GCAAG
seq0003        GCGCATACCGTAAGGGACACCGAACGCCCAGCCCGAACCAAAGGCCGGGGCAAG
seq0004        -------------------------------------------------GCAAG
seq0005        -------------------------------------------------GCAAG
seq0006        -------------------------------------------------GCAAG
seq0007        -------------------------------------------------GCAAG
seq0008        -------------------------------------------------ACACG
seq0009        -------------------------------------------------ACAAG
seq0013        -------------------------------------------------ACATT
seq0014        -------------------------------------------------ACTTG
seq0015        -------------------------------------CCATCGTCTCCACGCCG
seq0018        -------------------------------------------------TCAAG
seq0020        -------------------------------------------------CATGA


<<<<< 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, -13) .

[ 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0003   	    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
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   37  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   49
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1



(position)	   50   51   52   53

seq0000   	    0    0    0  -12
seq0001   	    0    0    0  -12
seq0002   	    0    0    0  -12
seq0003   	    0    0    0  -12
seq0004   	    0    0    0  -12
seq0005   	    0    0    0  -12
seq0006   	    0    0    0  -12
seq0007   	    0    0    0  -12
seq0008   	    0    0    0  -12
seq0009   	    0    0    0  -12
seq0013   	    0    0    0  -12
seq0014   	    0    0    0  -12
seq0015   	  -12  -12  -12  -12
seq0018   	    0    0    0  -12
seq0020   	   -1   -1  -13  -13



<<<<< 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	37	53	23	5,2	37,-12	0	12
1	49	49	27	6	49	n/a	0,1,2,4,5,6,7,8,9,10,11,13
2	49	53	28	3,0	-1,-13	0	14
3	53	53	27	1	-12	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13



<<<<< 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	0	1	0	0
1	1	0	0	1	0	0
2	2	0	0	1	0	0
3


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


[ 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	66	17	Complex(???)	23:53:64:-	22:37:48:X
1	0	1	1	Complex(???)	5:1:49:-	6:37:48:X
2	0	17	5	Complex	27:0:0:-/28:66:66:-	25:37:48:-
3	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

27:0:0	2
5:1:49	1
23:53:64	0
28:66:66	2


[ Contents of %indel_rec2assoc_cblks ]

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

5:0:36	None
25:37:48	2
22:37:48	0
18:37:48	None
14:37:48	None
6:37:48	1
4:37:48	None
3:37:48	None


<<<< (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} = 1) ]

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

3	=> [0],


[ Contents of %cb2hard_linking (#{keys} = 1) ]

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

0	=> [3],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

