<<<<< 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 = 115 ,
#{Sites in the segment}_rec = 115 .


<< 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)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        AT-TCATCCACAAGGGAGGAAGTGGCGGGCTCATGGATGAGTGCTCAGATAGCGTGTGCA
seq0001        AT-TCATCCACAAGGGAGGAAGTGGCGGGCTCATGGATGAGTGCTCAGATAGCGTGTGCA
seq0002        AT-TCATGCACAGGGGAGGAAGTGGCGGGCTCATGGATGAGTGGTCAGATAGCGTGTGCA
seq0003        AT-TCATGCACAGGGGAGGAAGTGGCGGGCTCATGGATCAGTGGTCAGATAGCGTGTGCA
seq0004        AT-TCGTGCACAGGGGAGGAAGTGGCGGGCTCATGGATGAGTGGTCAGATAGCGTGTGCA
seq0005        AT-TCATGCACAAGGGAGGAAGTGGCGGGCTCTTGGACGAGTGCTCAGATAGCGTGTGCA
seq0006        AT-TCATGCACAAGGGAGGAAGTGGCGGGCTCTTGGAGGAGTGCTCAGATAGCGTGTGCA
seq0007        ATTTCATGCACAAGTGAGGAAGTGGCGGGCTCTTCGACGAGTGTTCAGATAGCGTGTGCA
seq0008        AT-TGCTGCACAAGGGAGGAAGTAGCCGACTCTTTTATGAGTGATCAGATAGCGTGTGCA
seq0009        AT-ACCTGCACAAGGGAGGAAGTAGCGGACTCTTGTATAAGTGATCAGATACCCTGTGCA
seq0013        AG-ACTAG----------------------------------------------------
seq0014        AT-ACATG----------------------------------------------------
seq0015        AG-ATTCG----------------------------------------------------
seq0018        -G-ACCTG----------------------------------------------------
seq0020        -G-ACATG----------------------------------------------------

(position)     0000000000000000000000000000000000000000111111111111111
               6666666666777777777788888888889999999999000000000011111
               0123456789012345678901234567890123456789012345678901234
                                                                      
seq0000        TCACGAACTTCAACCTTAGATTTTATGTAACAAGGCAATCCCCGTACCGTGTCGG
seq0001        TCACGAACTGCAACCTTAGAGTTTATGTAACAAGGCAATCCCCGTACCGTGTCGG
seq0002        TCAGGAACTGCAACCTTAGAGGTT-TGTCACAAGGCAA--------CCGTGTCGG
seq0003        TCAGGAACTGCAACCTTAGAGTTT-TGTCACAAGGCAA--------GCGTGTCGG
seq0004        TCAGGAACTGCAACCTTAGAGTTT-TGTCACAAGGCAA--------GCGTGTCGG
seq0005        TAACGAACGGCAC-CTTAGATTTT-TGTAACAAGGCAA--------CAATGTCGG
seq0006        TCACGAACTGCACCCTTAGATTTT-TGTAACAAGGCAA--------CAATGTCGG
seq0007        TCACGAACTGCGCCCTTAGATTTT-TGTTACAAGGCAA--------CAATGTCGG
seq0008        ACACGAACTGTGACCTTTAATTTT-GGTAAAAAGGCAT--------CAGTGTT-G
seq0009        ACGCGAACTGTAACCTTTG------------------------------------
seq0013        -------------------------------------------------------
seq0014        -------------------------------------------------------
seq0015        -------------------------------------------------------
seq0018        -------------------------------------------------------
seq0020        -------------------------------------------------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        A-TTCATCCACAAGGGAGGAAGTGGCGGGCTCATGGATGAGTGCTCAGATAGCGTGTGCA
seq0001        A-TTCATCCACAAGGGAGGAAGTGGCGGGCTCATGGATGAGTGCTCAGATAGCGTGTGCA
seq0002        A-TTCATGCACAGGGGAGGAAGTGGCGGGCTCATGGATGAGTGGTCAGATAGCGTGTGCA
seq0003        A-TTCATGCACAGGGGAGGAAGTGGCGGGCTCATGGATCAGTGGTCAGATAGCGTGTGCA
seq0004        A-TTCGTGCACAGGGGAGGAAGTGGCGGGCTCATGGATGAGTGGTCAGATAGCGTGTGCA
seq0005        A-TTCATGCACAAGGGAGGAAGTGGCGGGCTCTTGGACGAGTGCTCAGATAGCGTGTGCA
seq0006        A-TTCATGCACAAGGGAGGAAGTGGCGGGCTCTTGGAGGAGTGCTCAGATAGCGTGTGCA
seq0007        ATTTCATGCACAAGTGAGGAAGTGGCGGGCTCTTCGACGAGTGTTCAGATAGCGTGTGCA
seq0008        A-TTGCTGCACAAGGGAGGAAGTAGCCGACTCTTTTATGAGTGATCAGATAGCGTGTGCA
seq0009        A-TACCTGCACAAGGGAGGAAGTAGCGGACTCTTGTATAAGTGATCAGATACCCTGTGCA
seq0013        A--------------------------GACTA----------------------------
seq0014        A--------------------------TACAT----------------------------
seq0015        A--------------------------GATTC----------------------------
seq0018        ---------------------------GACCT----------------------------
seq0020        ---------------------------GACAT----------------------------

(position)     0000000000000000000000000000000000000000111111111111111
               6666666666777777777788888888889999999999000000000011111
               0123456789012345678901234567890123456789012345678901234
                                                                      
seq0000        TCACGAACTTCAACCTTAGATTTTATGTAACAAGGCAATCCCCGTACCGTGTCGG
seq0001        TCACGAACTGCAACCTTAGAGTTTATGTAACAAGGCAATCCCCGTACCGTGTCGG
seq0002        TCAGGAACTGCAACCTTAGAGGTT-TGTCACAAGGCAA--------CCGTGTCGG
seq0003        TCAGGAACTGCAACCTTAGAGTTT-TGTCACAAGGCAA--------GCGTGTCGG
seq0004        TCAGGAACTGCAACCTTAGAGTTT-TGTCACAAGGCAA--------GCGTGTCGG
seq0005        TAACGAACGGCA-CCTTAGATTTT-TGTAACAAGGCAA--------CAATGTCGG
seq0006        TCACGAACTGCACCCTTAGATTTT-TGTAACAAGGCAA--------CAATGTCGG
seq0007        TCACGAACTGCGCCCTTAGATTTT-TGTTACAAGGCAA--------CAATGTCGG
seq0008        ACACGAACTGTGACCTTTAATTTT-GGTAAAAAGGCAT--------CAGTGT-TG
seq0009        ACGCGAACTGTAACCTT------------------------------------TG
seq0013        ------------------------------------------------------G
seq0014        ------------------------------------------------------G
seq0015        ------------------------------------------------------G
seq0018        ------------------------------------------------------G
seq0020        ------------------------------------------------------G


<<<<< 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, 0) .

[ 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    -    1    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
seq0001   	    0    -    1    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
seq0002   	    0    -    1    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
seq0003   	    0    -    1    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   	    0    -    1    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
seq0005   	    0    -    1    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
seq0006   	    0    -    1    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
seq0007   	    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
seq0008   	    0    -    1    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
seq0009   	    0    -    1    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
seq0013   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   25   25   25   25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    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
seq0001   	    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
seq0002   	    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    -    -
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    -    -
seq0004   	    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    -    -
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    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    0    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    0    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    0    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    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114

seq0000   	    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
seq0002   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    0    0    0    0    0    0    -    1    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -  107



<<<<< 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} = 6) >>

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

0	2	2	19	3	1	n/a	0,1,2,3,4,5,6,8,9
1	27	31	29	7,6	26,25	0	10,11,12,13,14
2	73	73	10	5	1	n/a	5
3	113	113	16	4	1	n/a	8
4	113	114	17	8	36	n/a	9
5	114	114	29	9	107	n/a	10,11,12,13,14



<<<<< 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} = 6) >>>>>


[[ 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	0	2	0	0	0	0
2	1	1	0	0	0	0
3	0	0	0	1	0	0
4	1	1	0	0	0	0
5	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	Shift	12:2:2:-	12:1:1:-
1	0	6	5	Complex(???)	None	19:2:26:-/19:32:113:-
2	0	1	1	Shift	10:73:73:X	10:72:72:X
3	0	1	1	NO_ASSOCIATED_EVENT(???)	None	17:77:111:X
4	0	2	2	Shift	17:79:114:X	17:77:111:X
5	0	1	1	Complex(???)	19:8:114:-	19:32:113:-


[ Contents of %indel_ref2assoc_cblks ]

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

25:0:0	{Equivalent to '25:0:0'(rec)}
12:2:2	0
19:8:114	5
10:73:73	2
17:79:114	4
3:84:84	{Equivalent to '3:84:84'(rec)}
3:98:105	{Equivalent to '3:98:105'(rec)}
15:113:113	None


[ Contents of %indel_rec2assoc_cblks ]

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

25:0:0	{Equivalent to '25:0:0'(ref)}
12:1:1	0
19:2:26	1
19:32:113	1,5
10:72:72	2
17:77:111	3,4
3:84:84	{Equivalent to '3:84:84'(ref)}
3:98:105	{Equivalent to '3:98:105'(ref)}
15:112:112	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} = 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} = 1) ]

Indx_cblk_A	indx_cblk_B

1	5


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

[ For the 1 th pair: (1, 5) ]


{ The representative path is: 1  -> 5 }


( 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)	27	32	26	25	19	10,11,12,13,14	10,11,12,13,14
2nd(reconstructed)	114	114	82	82	19	10,11,12,13,14	10,11,12,13,14


( 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)	Split(same-type)	19:8:114:-	19:2:26:-/19:33:114:-
2nd(reconstructed)	Shift	19:33:114:-	19:32:113:-


