<<<<< 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 = 170 ,
#{Sites in the segment}_rec = 133 .


<< 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        CCAGAG--GTTC------TCGTTTGACGGCCACTGCC---ATGTGCACAGAGTGAC--C-
seq0001        CGAGAG--TTTC------TCGTTTGACGGCCACTGAC---ATGTGCACAGAGTGAC--C-
seq0002        CGAGAG--GTTC------TCGTTTTACGGCCACTGAC---ATGTGCACAGAGTGAC--C-
seq0003        CGAGAG--GTTC------TCGTTTGACGGCCACTGAC---ATGTGCACAGAGTGAC--C-
seq0004        CGAGAG--GTTC------TCGTTTGACGGCCTCTGAC---ATGTGCACAGAGTGAC--C-
seq0005        CGAGAG--TTTC------TCGTTCGACGTCCACTGAC---ATGTGCCCAGAGTGATCTG-
seq0006        CGGGAG--TTTC------TCGTTTGACGCCCACTGACGTCATGTGCCCAGAGTGATCTG-
seq0007        CGGGAG--TTTC------TCGTTTGACGTCCACTGACGTCATGTGCCCAGAGTGATCTG-
seq0008        GGAGAG--CATC-----CTTGTTTGACGGCCACGG-------CTGCACAGAGTGACCTC-
seq0009        GGGCAG--CTTC-----CTTGATTGACTGCCCCGG-------CTGCACAGAGTGATCTC-
seq0013        ACCGTGTCATTCCGCCA-TTGTTTGACGGCCACTG-------CTCCACCGAGTGTTACCA
seq0014        TC--------------------------------------------------TGACGTCA
seq0015        TCAGAGGATTCC------TTGTATCACGGCCACTG-------CT--AAAGAGTGACTTTA
seq0018        -CAGAGTCTTTC------GTGCTTGACTGCCAATG-------CTGCACAAAATGACTTC-
seq0020        -GAGAGTCGCTC------TTGCCAGTCGGA-ACTG-------CTGCACAGAGTGACTAC-

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------AG----------------------------
seq0001        ------------------------------AG----------------------------
seq0002        ------------------------------AG----------------------------
seq0003        ------------------------------AG----------------------------
seq0004        ------------------------------AG----------------------------
seq0005        ------------------------------AG----------------------------
seq0006        ------------------------------AG----------------------------
seq0007        ------------------------------AG----------------------------
seq0008        ------------------------------AG----------------------------
seq0009        ------------------------------AG----------------------------
seq0013        GGA------ACATCCCTTCCTCTGTCCCTAAGTGAGTTGTCGAAATAGGCACAGAACAAT
seq0014        GGA------GTAGCCCCACGTCTGCCCC-AAC----------------------------
seq0015        GGAGACTCTGTAGCCCTACGGCTGTCCC-AGG----------------------------
seq0018        ------------------------------AA----------------------------
seq0020        ------------------------------TG----------------------------

(position)     11111111111111111111111111111111111111111111111111
               22222222223333333333444444444455555555556666666666
               01234567890123456789012345678901234567890123456789
                                                                 
seq0000        ------TC-GGTAACG--------------------------------TT
seq0001        ------TC-GGTAACG--------------------------------TT
seq0002        ------TC-GGTAACG--------------------------------AT
seq0003        ------TC-GGTAACG--------------------------------AT
seq0004        ------TGCGGTAACG--------------------------------AT
seq0005        ------TG-GGTAACG--------------------------------TT
seq0006        ------TG-GGTAACG--------------------------------CT
seq0007        ------TG-GGTAACG--------------------------------TT
seq0008        ------TC-AGTAA----------------------------------TT
seq0009        ------AC-AGTAACG----------------------------------
seq0013        AGGAAA---------G--------------------------------TT
seq0014        ------TG-AGTAAGG--------------------------------TT
seq0015        ------GC-GGTAAGGAGACAACTTTTCTCAGTACATTCACGCCTATTTT
seq0018        ------TC-GGTAACG--------------------------------TT
seq0020        ------TC-GGTAACA--------------------------------TT


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CCAGAG-------GTTCTCGTTTGACGGCCACTGC---CATGTGCACAGAGTGACC--AG
seq0001        CGAGAG-------TTTCTCGTTTGACGGCCACTGA---CATGTGCACAGAGTGACC--AG
seq0002        CGAGAG-------GTTCTCGTTTTACGGCCACTGA---CATGTGCACAGAGTGACC--AG
seq0003        CGAGAG-------GTTCTCGTTTGACGGCCACTGA---CATGTGCACAGAGTGACC--AG
seq0004        CGAGAG-------GTTCTCGTTTGACGGCCTCTGA---CATGTGCACAGAGTGACC--AG
seq0005        CGAGAG-------TTTCTCGTTCGACGTCCACTGA---CATGTGCCCAGAGTGATCTGAG
seq0006        CGGGAG-------TTTCTCGTTTGACGCCCACTGACGTCATGTGCCCAGAGTGATCTGAG
seq0007        CGGGAG-------TTTCTCGTTTGACGTCCACTGACGTCATGTGCCCAGAGTGATCTGAG
seq0008        GGAGAGC------ATCCTTGTTTGACGGCCACGGC-------TGCACAGAGTGACCTCAG
seq0009        GGGCAGC------TTCCTTGATTGACTGCCCCGGC-------TGCACAGAGTGATCTCAG
seq0013        ACCGTGTCATTCCGCCATTGTTTGACGGCCACTGC-------TCCACCGAGTGTTACCAG
seq0014        TCTGACG---TCAGGAGTAGCCCCACGTC-------------TGCCCCAACTGA------
seq0015        TCAGAGG-----ATTCCTTGTATCACGGCCACTGC------T---AAAGAGTGACTTTAG
seq0018        CAGAGTC------TTTCGTGCTTGACTGCCAATGC-------TGCACAAAATGACTTCAA
seq0020        GAGAGTC------GCTCTTGCCAGTCGGA-ACTGC-------TGCACAGAGTGACTACTG

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        T-----------------------------------------------------------
seq0001        T-----------------------------------------------------------
seq0002        T-----------------------------------------------------------
seq0003        T-----------------------------------------------------------
seq0004        T-----------------------------------------------------------
seq0005        T-----------------------------------------------------------
seq0006        T-----------------------------------------------------------
seq0007        T-----------------------------------------------------------
seq0008        T-----------------------------------------------------------
seq0009        A-----------------------------------------------------------
seq0013        G------AACATCCCTTCCTCTGTCCCTAAGTGAGTTGTCG--AAATAGGCACAGAACA-
seq0014        ------------------------------------------------------------
seq0015        GAGACTCTGTAGCCCTACGGCTGTCCCAGGGCGGTAAGGAGACAACTTTTCTCAGTACAT
seq0018        T-----------------------------------------------------------
seq0020        T-----------------------------------------------------------

(position)     1111111111111
               2222222222333
               0123456789012
                            
seq0000        ---CGGTAACGTT
seq0001        ---CGGTAACGTT
seq0002        ---CGGTAACGAT
seq0003        ---CGGTAACGAT
seq0004        --GCGGTAACGAT
seq0005        ---GGGTAACGTT
seq0006        ---GGGTAACGCT
seq0007        ---GGGTAACGTT
seq0008        ---CAGTAA--TT
seq0009        ---CAGTAA--CG
seq0013        --ATAGGAAAGTT
seq0014        -----GTAAGGTT
seq0015        TCACGCCTATTTT
seq0018        ---CGGTAACGTT
seq0020        ---CGGTAACATT


<<<<< 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, -37) .

[ 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    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0001   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0002   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0003   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0004   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0005   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0006   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0007   	    0    0    0    0    0    0    -    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0008   	    0    0    0    0    0    0   -2    -    -    -    -    -    -    4    4    4   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -8    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1
seq0009   	    0    0    0    0    0    0   -2    -    -    -    -    -    -    4    4    4   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -8    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -8    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1
seq0014   	    0    0  -50  -50  -50  -50  -50    -    -    -  -47  -47  -47  -47  -47  -47  -53  -53  -53  -53  -53  -53  -53  -53  -53  -53  -53  -53  -53    -    -    -    -    -    -    -    -    -    -    -    -    -  -40  -40  -40  -40  -40  -40  -41  -41
seq0015   	    0    0    0    0    0    0    0    -    -    -    -    -    5    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -8    -    -    -    -    -    -   -2    -    -    -   -1   -1   -1   -1   -1
seq0018   	   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -8    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1
seq0020   	   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    5    5    5    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -   -1   -1   -1   -1   -8    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1



(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   	   -1   -1   -1   -1   -1   -3    -    -  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -1   -1   -1   -1   -1   -3    -    -  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -1   -1   -1   -1   -1   -3    -    -  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -1   -1   -1   -1   -1   -3    -    -  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -1   -1   -1   -1   -1   -3    -    -  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    5   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0014   	  -41  -75  -75  -76    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2  -36  -36  -37  -37  -37  -37  -37  -37  -37  -37
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -1   -1   -1   -1   -1   -1   -1   -1  -32  -32  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5    -    -  -37  -37
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5    -    -   -3   -3
seq0013   	   -1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    4    4    4    4    4    4    4    4   -5  -37  -37
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5  -37  -37
seq0015   	  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37  -37
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -5   -5   -5   -5   -5   -5   -5  -37  -37



<<<<< 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} = 28) >>

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

0	0	6	29	25	-1	n/a	13,14
1	2	28	21	4,5,3	-50,-47,-53	0,0	11
2	6	6	18	21	-2	n/a	8,9
3	12	16	23	40	5	n/a	12
4	13	16	29	39	5	n/a	0,1,2,3,4,5,6,7,13,14
5	13	33	18	37,28	4,-1	0	8,9
6	17	34	15	27	-1	n/a	0,1,2,3,4,5
7	17	33	29	24	-1	n/a	10,12,13,14
8	17	57	13	34	-1	n/a	6,7
9	34	34	29	12	-8	n/a	8,9,10,12,13,14
10	38	38	15	36	2	n/a	0,1,2,3,4,5
11	39	54	9	30	-1	n/a	0,1,2,3,4
12	39	57	10	33	-1	n/a	5
13	41	41	23	22	-2	n/a	12
14	42	129	20	31,41,32,35,38	-1,5,-1,1,4	0,0,0,0	10
15	42	53	21	7,6,1,0	-40,-41,-75,-76	0,0,0	11
16	42	57	29	26	-1	n/a	8,9,13,14
17	45	132	23	29,23,10,9	-1,-2,-36,-37	0,0,0	12
18	55	55	9	19	-3	n/a	0,1,2,3,4
19	58	60	29	11,2	-32,-66	0	0,1,2,3,4,5,6,7,8,9,13,14
20	122	130	6	17	-5	n/a	4
21	123	123	29	18	-4	n/a	0,1,2,3,5,6,7,8,9,13,14
22	124	130	29	13	-5	n/a	0,1,2,3,5,6,7,13,14
23	124	128	18	14	-5	n/a	8,9
24	125	130	21	15	-5	n/a	11
25	130	130	20	16	-5	n/a	10
26	131	132	29	8	-37	n/a	0,1,2,3,4,5,6,7,8,10,11,13,14
27	131	132	17	20	-3	n/a	9



<<<<< 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} = 28) >>>>>


[[ 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	1	0	0
1	1	1	0	0	0	0
2	0	0	1	1	0	0
3	0	0	0	2	0	0
4	0	1	1	0	0	0
5	1	0	1	1	0	0
6	1	0	1	0	0	0
7	0	0	2	0	0	0
8	1	1	0	0	0	0
9	1	1	0	0	0	0
10	0	1	0	0	0	0
11	1	0	0	0	0	0
12	0	0	1	0	0	0
13	1	1	0	1	0	0
14	3	0	0	1	0	0
15	0	1	0	1	0	0
16
17	3	4	0	0	0	0
18	1	1	0	0	0	0
19	1	0	0	1	0	0
20	1	0	0	1	0	0
21	0	0	0	1	0	0
22	0	0	1	0	0	0
23	0	1	1	0	0	0
24	0	1	0	0	0	0
25	1	0	0	0	0	0
26
27	1	0	1	1	0	0


[ Skipped Composite-Blocks (#{cblocks} = 2): 16, 26 . ]


[ 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	7	7	Complex(???)	25:0:0:-/19:6:7:X	24:12:12:-
1	0	30	27	Complex(???)	21:2:51:X	21:29:34:X
2	0	1	1	Complex(???)	19:6:7:X	15:6:6:X
3	0	5	5	Complex	None	22:10:11:-/24:12:12:-
4	0	4	4	Complex(???)	19:6:7:X	24:12:12:-
5	0	26	21	Complex(???)	18:17:17:-/15:35:41:-	15:6:6:X
6	0	18	18	Complex(???)	15:35:41:-/18:17:17:-	None
7	0	17	17	Complex	18:17:17:-/15:35:41:-	None
8	0	41	41	Shift(???)	13:37:39:-	13:35:37:-
9	0	1	1	Complex(???)	15:35:41:-	15:38:40:-
10	0	1	1	Complex(???)	None	15:38:40:-
11	0	16	16	Complex(???)	9:56:57:X	None
12	0	19	19	NO_ASSOCIATED_EVENT(???)	13:37:39:-	None
13	0	1	1	Complex(???)	23:44:45:X	23:42:44:X/22:41:41:X
14	0	83	88	Complex	20:126:134:X/20:92:125:-/20:88:88:-	22:41:41:X
15	0	48	12	Complex(???)	None	21:54:124:X/22:41:41:X
16	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
17	0	124	88	Complex	23:44:45:X/23:63:68:-/23:136:167:-	23:42:44:X/23:61:66:-/23:101:102:-/23:119:121:-
18	0	1	1	Shift	9:56:57:X	9:56:57:X
19	0	37	3	Complex(???)	24:59:89:-	23:61:66:-
20	0	9	9	Complex(???)	6:128:128:-	5:122:122:X
21	0	1	1	NO_ASSOCIATED_EVENT(???)	None	25:122:122:-
22	0	7	7	NO_ASSOCIATED_EVENT(???)	23:136:167:-	None
23	0	5	5	Complex(???)	16:134:135:X	18:129:130:X
24	0	6	6	Complex(???)	None	21:54:124:X
25	0	1	1	Complex(???)	20:126:134:X	None
26	Skipped!!(NO_RELEVANT_BRANCH)
27	0	2	2	Neighboring-branch-Merge(2del)(?)	17:168:169:X/16:134:135:X	18:129:130:X


[ Contents of %indel_ref2assoc_cblks ]

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

25:0:0	0
21:2:51	1
19:6:7	0,2,4
20:12:16	None
18:17:17	5,6,7
27:30:30	None
15:35:41	5,6,7,9
13:37:39	8,12
23:44:45	13,17
9:56:57	11,18
24:59:89	19
23:63:68	17
20:88:88	14
20:92:125	14
20:126:134	14,25
6:128:128	20
16:134:135	23,27
23:136:167	17,22
17:168:169	27


[ Contents of %indel_rec2assoc_cblks ]

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

15:6:6	2,5
20:7:9	None
22:10:11	3
24:12:12	0,3,4
27:29:29	None
21:29:34	1
13:35:37	8
15:38:40	9,10
25:41:41	None
22:41:41	13,14,15
18:41:41	None
23:42:44	13,17
21:54:124	15,24
9:56:57	18
23:61:66	17,19
24:67:118	None
23:101:102	17
23:119:121	17
25:122:122	21
18:122:122	None
14:122:122	None
5:122:122	20
4:122:122	None
3:122:122	None
18:129:130	23,27


<<<< (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} = 3) ]

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

7	=> [5,6],
12	=> [8],
26	=> [17],


[ Contents of %cb2hard_linking (#{keys} = 4) ]

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

5	=> [7],
6	=> [7],
8	=> [12],
17	=> [26],


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

Indx_cblk_A	indx_cblk_B

18	11
27	23


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

[ For the 1 th pair: (18, 11) ]

[ For the 2 th pair: (27, 23) ]

