<<<<< 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 = 109 ,
#{Sites in the segment}_rec = 61 .


<< 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        ----------CAA---CC---ATGTGC---TTAGACCGA--CTCAGACGGGTAGGAGGGG
seq0001        ----------CAA---CC---ATGTGC---TTAGACCGA--CTCAGACGGGTAGGAGGGG
seq0002        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGAGGGG
seq0003        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGGGGGG
seq0004        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGAGGGG
seq0005        ----------CAA---CG---ATGTGC---TTTGACCGA--CTCAGAAGGGTAGGAGGGG
seq0006        ----------CAA---CC---ATGTGC---TTTGACCGAACCTCAGACGGGTAGGAGGTG
seq0007        ----------CAA---CC---ATGTGC---GTTGACCGA--CTCAGACGGGTAGGAGGGG
seq0008        ----------CAA---CC---GTGTGC---TAT---------------------------
seq0009        ----------CAAGGACC---TGGCGC---TTC---------------------------
seq0013        ----------TAA---AC---GTGCGCCTATTT---------------------------
seq0014        ----------TAA---CC---GTTGGC---TTT---------------------------
seq0015        ----------TAA---CC----TGGGC---CTT---------------------------
seq0018        ----------CAA---CC---GAGTG----AGT---------------------------
seq0020        CACACTTAGTCAA---CGTCGGTGTGC---ATT---------------------------

(position)     0000000000000000000000000000000000000000111111111
               6666666666777777777788888888889999999999000000000
               0123456789012345678901234567890123456789012345678
                                                                
seq0000        GTCGGG------------------------------------ATACTTC
seq0001        GTCGGG------------------------------------ATACTTC
seq0002        GTCGGG------------------------------------ATTCTTC
seq0003        GTCGGG------------------------------------ATTCTTC
seq0004        GTCGGG------------------------------------ATTCTTC
seq0005        GTCGGG------------------------------------ATCCTGC
seq0006        GTCGGG------------------------------------ATCCTTC
seq0007        GTCGGG------------------------------------GTCCTTC
seq0008        -TCGGGAAGGCGCCCCCCGGACGCTGACCATGACCCCGGTAAATTC---
seq0009        ---GGA------------------------------------ATTC---
seq0013        -TCCTG------------------------------------AGCC---
seq0014        -TCCAG------------------------------------ATCC---
seq0015        -TCCGC------------------------------------ATCA---
seq0018        -TCGGG------------------------------------ATC----
seq0020        -TCG--------------------------------------ATCC---


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CAACCATGTGCTTA-------GACCGA--CTCAGACGGGTAGGAGGGGGTCGGGATACTT
seq0001        CAACCATGTGCTTA-------GACCGA--CTCAGACGGGTAGGAGGGGGTCGGGATACTT
seq0002        CAACCATGTGCTTT-------GACCGA--CTCAGACGGCTAGGAGGGGGTCGGGATTCTT
seq0003        CAACCATGTGCTTT-------GACCGA--CTCAGACGGCTAGGGGGGGGTCGGGATTCTT
seq0004        CAACCATGTGCTTT-------GACCGA--CTCAGACGGCTAGGAGGGGGTCGGGATTCTT
seq0005        CAACGATGTGCTTT-------GACCGA--CTCAGAAGGGTAGGAGGGGGTCGGGATCCTG
seq0006        CAACCATGTGCTTT-------GACCGAACCTCAGACGGGTAGGAGGTGGTCGGGATCCTT
seq0007        CAACCATGTGCGTT-------GACCGA--CTCAGACGGGTAGGAGGGGGTCGGGGTCCTT
seq0008        CAACCGTGTGCTATTCGGGAAGGCGCC--CCCCGGACGCTGACCATGACCCCGGTAAATT
seq0009        CAA-------------------------------------GGACCTGGCGCTTCGGAATT
seq0013        TAAACGTGCGCCTA-----------------------------------TTTTCCTGAGC
seq0014        TAACCGTTGGCTTT--------------------------------------TCCAGATC
seq0015        TAACCTGGGCCTT---------------------------------------TCCGCATC
seq0018        CAACCGAGTGAGT----------------------------------------TCGGGAT
seq0020        CACACTTAGTCAA---------------------------CGTCGGTGTGCATTTCGATC

(position)     6
               0
                
seq0000        C
seq0001        C
seq0002        C
seq0003        C
seq0004        C
seq0005        C
seq0006        C
seq0007        C
seq0008        C
seq0009        C
seq0013        C
seq0014        C
seq0015        A
seq0018        C
seq0020        C


<<<<< 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, -48) .

[ 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   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0001   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0002   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0003   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0004   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0005   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0006   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0007   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -  -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
seq0008   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45
seq0009   	  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   27   27   27   24   24   24   24   24
seq0013   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -16  -16  -16    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   19
seq0014   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -16  -19  -19  -19    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	  -10  -10  -10  -13  -13  -17  -17  -17  -17  -17  -20  -20  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	  -10  -10  -10  -13  -13  -16  -16  -16  -16  -16  -20  -20  -20    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   24   24   24   24   24   24   24   24   24   24



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

seq0000   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0001   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0002   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0003   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0004   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0005   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0006   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0007   	  -12  -12  -12  -12  -48  -48  -48  -48  -48  -48  -48
seq0008   	  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45
seq0009   	   24   21   21   21   -9   -9   -9  -45  -45  -45  -45
seq0013   	   19   19   -9   -9   -9   -9   -9  -45  -45  -45  -45
seq0014   	    -    -   -9   -9   -9   -9   -9  -45  -45  -45  -45
seq0015   	    -    -   -9   -9   -9   -9   -9  -45  -45  -45  -45
seq0018   	    -    -    -   -8   -8   -8   -8   -8  -44  -44  -44
seq0020   	   24   21   21   21   -7   -7   -7  -45  -45  -45  -45




[INFORMATION] The original $commoner_shift_flank = -48. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   38   38
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48



(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   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0001   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0002   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0003   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0004   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0005   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0006   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0007   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -   36   36   36   36   36   36    -    -   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36   36
seq0008   	   38   35   35   32   32   32   32   32   32   29   29   29    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0009   	   38    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   75   75   75   75   75   72   72   72   72   72   72   69
seq0013   	   38   35   35   32   32   32   32   32   32   32   32   32    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   67   67   67
seq0014   	   38   35   35   32   32   32   32   32   32   29   29   29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	   38   35   35   31   31   31   31   31   28   28   28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	   38   35   35   32   32   32   32   32   28   28   28    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   48   48   48   48   48   48   48   48   48   48   48    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   72   72   72   72   72   72   72   72   72   72   72   69



(position)	  100  101  102  103  104  105  106  107  108

seq0000   	   36   36    0    0    0    0    0    0    0
seq0001   	   36   36    0    0    0    0    0    0    0
seq0002   	   36   36    0    0    0    0    0    0    0
seq0003   	   36   36    0    0    0    0    0    0    0
seq0004   	   36   36    0    0    0    0    0    0    0
seq0005   	   36   36    0    0    0    0    0    0    0
seq0006   	   36   36    0    0    0    0    0    0    0
seq0007   	   36   36    0    0    0    0    0    0    0
seq0008   	    3    3    3    3    3    3    3    3    3
seq0009   	   69   69   39   39   39    3    3    3    3
seq0013   	   39   39   39   39   39    3    3    3    3
seq0014   	   39   39   39   39   39    3    3    3    3
seq0015   	   39   39   39   39   39    3    3    3    3
seq0018   	    -   40   40   40   40   40    4    4    4
seq0020   	   69   69   41   41   41    3    3    3    3



<<<<< 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... >>>>>

... The MINI-classes increased by 2 compared to the old set!! ...


<<<<< 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} = 19) >>

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

0	48	50	27	13	38	n/a	0,1,2,3,4,5,6,7,8,9,10,11,12,13
1	48	60	28	18	48	n/a	14
2	51	52	27	11	35	n/a	0,1,2,3,4,5,6,7,8,10,11,12,13
3	53	58	25	8	32	n/a	0,1,2,3,4,5,6,7,8,11
4	53	61	20	10	32	n/a	10
5	53	60	23	7,5	31,28	0	12
6	53	57	26	9	32	n/a	13
7	58	60	26	4	28	n/a	13
8	59	61	25	6	29	n/a	0,1,2,3,4,5,6,7,8,11
9	62	108	16	0,2	1,3	0	8
10	69	101	15	12	36	n/a	0,1,2,3,4,5,6,7
11	88	101	28	22,20	72,69	0	14
12	88	101	17	24,23,21	75,72,69	0,0	9
13	97	99	20	19	67	n/a	10
14	100	104	24	14	39	n/a	10,11,12
15	101	108	26	16,3	40,4	0	13
16	102	104	28	17	41	n/a	14
17	102	104	17	15	39	n/a	9
18	105	108	29	1	3	n/a	9,10,11,12,14



<<<<< 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} = 19) >>>>>


[[ 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	0	0	0
1	1	0	0	1	0	0
2	1	0	0	0	0	0
3	0	0	2	0	0	0
4	1	0	0	0	0	0
5	1	1	0	0	0	0
6	1	0	1	0	0	0
7	1	0	0	1	0	0
8	0	1	0	0	0	0
9	1	1	1	0	0	0
10	1	0	0	1	0	0
11	1	0	0	1	0	0
12	1	1	0	0	0	0
13	1	0	0	1	0	0
14	0	0	0	1	0	0
15	1	1	0	0	0	0
16	1	0	0	0	0	0
17	1	0	1	0	0	0
18	1	0	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	3	3	Complex(???)	28:0:9:-	None
1	0	13	13	Complex(???)	28:0:9:-	25:61:61:-
2	0	2	2	Complex(???)	28:18:20:-	None
3	0	6	6	Complex	28:18:20:-/26:26:26:X	None
4	0	9	9	Complex(???)	20:27:29:-	None
5	0	11	8	Complex(???)	23:21:21:X	23:61:99:X
6	0	5	5	Complex(???)	26:26:26:X/28:18:20:-	None
7	0	3	3	Complex(???)	26:26:26:X	25:61:61:-
8	0	3	3	Complex(???)	None	25:61:61:-
9	0	45	47	Complex(???)	16:66:101:-/17:61:62:X	16:62:68:-
10	0	33	33	Complex(???)	15:33:60:-	19:69:87:-
11	0	17	14	Complex(???)	28:18:20:-	26:88:100:X
12	0	20	14	Complex(???)	17:13:15:-	17:51:87:X
13	0	3	3	Complex(???)	20:27:29:-	21:97:99:X
14	0	5	5	NO_ASSOCIATED_EVENT(???)	None	23:61:99:X
15	0	44	8	Complex(???)	26:105:105:X	26:88:100:X
16	0	3	3	Complex(???)	27:64:65:-	None
17	0	3	3	Complex(???)	17:61:62:X/16:66:101:-	None
18	0	4	4	Complex(???)	15:106:108:-	None


[ Contents of %indel_ref2assoc_cblks ]

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

28:0:9	0,1
17:13:15	12
28:18:20	2,3,6,11
23:21:21	5
26:26:26	3,6,7
20:27:29	4,13
15:33:60	10
11:39:40	{Equivalent to '11:75:76'(rec)}
17:61:62	9,17
27:64:65	16
16:66:101	9,17
26:105:105	15
15:106:108	18


[ Contents of %indel_rec2assoc_cblks ]

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

17:51:87	12
25:61:61	1,7,8
23:61:99	5,14
16:62:68	9
19:69:87	10
11:75:76	{Equivalent to '11:39:40'(ref)}
26:88:100	11,15
24:88:96	None
21:97:99	13


<<<< (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]

6	=> [3],


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

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

3	=> [6],


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

Indx_cblk_A	indx_cblk_B

4	13
9	17


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

[ For the 1 th pair: (4, 13) ]

[ For the 2 th pair: (9, 17) ]

