<<<<< 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 = 86 ,
#{Sites in the segment}_rec = 80 .


<< 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        GGAAGTCTG--CGGCT------------------------------TACGG-ACAGCGTT
seq0001        GGAAGTCTG--CGGCT------------------------------TACGG-ACAGCGTT
seq0002        GGCAGTCTG--CGTCT------------------------------TAGGGTACAGCGTT
seq0003        GGCAGTCTG--CGGCT------------------------------TAGGGTACAGCGTT
seq0004        GGCAGTCTG--CGGCT------------------------------TAGGGTACAGCGTT
seq0005        GGAAGTCTG--CGGCT------------------------------TAGGGAACAGCGTT
seq0006        GGAAGTCTG--TGGCT------------------------------TAGGGTACAGCGTT
seq0007        GGAAGTCTG--CGCCT------------------------------TAGGGTACAGCGTT
seq0008        GGGAGTCCG--TAGAG-GGGTTGT--------GAGTACT----TC-TAAGGTACA-CGTT
seq0009        TGGTGTCCG--TGGAG-GGGGTGT--------GAGTACT----TCGTAAGGTACAGCGTT
seq0013        GGGAGTC------GAGCGAGTTGTCAACAGTAAAATACT----TC-TAGGATACAACGGT
seq0014        GGGAGTCCG--TGGAG-GAATTGTCAACAGACAATTACT----TC-TAAGGTACGAGGGT
seq0015        ------------------------------------------------------------
seq0018        GGGAGTCTGAT-----------GTCAACCGTCGTCTACTAATCTC-TACGGTACGGCGCT
seq0020        GAGAGTCTG--TGGAG-GAGTGGCCAACTA-C-ACTGCTAACCTC-TAAG---CTGCGTT

(position)     66666666667777777777888888
               01234567890123456789012345
                                         
seq0000        CTCCGAAACAAA-GGATATCCGCAGA
seq0001        CTCCGAAACAAA-GAATATCCGCAGA
seq0002        CTCCGAAACAAC-GGATATCTGCAGA
seq0003        CTCCGAAACAAC-GGATATCTGCAGA
seq0004        CTCCGAAACAAC-GGATATCTGCAGA
seq0005        CTCTAAAACAAA-GGATATCCGCCGA
seq0006        CTCCAAAACAAA-GGATATCCGCCGA
seq0007        CTCCGAAACAAA-GGATATCCGCCGA
seq0008        ATCCGATACAAA-GGGAATCCGCAGA
seq0009        CTCCGATACAAA-GGGCATCCGCAGA
seq0013        -TCCGTGAGACACGGATATCCGGAGT
seq0014        TACCGATACAAA-GGTTAGCCGCAAA
seq0015        --------------------------
seq0018        G--CGAAACAAG-TGATAGCCGCAGA
seq0020        T--TGATACAAA-GGA--GCCCCACA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GGAAGTCTGCGGCT---------------------------TACGG-ACAGCGTTCTCCG
seq0001        GGAAGTCTGCGGCT---------------------------TACGG-ACAGCGTTCTCCG
seq0002        GGCAGTCTGCGTCT---------------------------TAGGGTACAGCGTTCTCCG
seq0003        GGCAGTCTGCGGCT---------------------------TAGGGTACAGCGTTCTCCG
seq0004        GGCAGTCTGCGGCT---------------------------TAGGGTACAGCGTTCTCCG
seq0005        GGAAGTCTGCGGCT---------------------------TAGGGAACAGCGTTCTCTA
seq0006        GGAAGTCTGTGGCT---------------------------TAGGGTACAGCGTTCTCCA
seq0007        GGAAGTCTGCGCCT---------------------------TAGGGTACAGCGTTCTCCG
seq0008        GGGAGTCCGTAGAGGGGTTGT----------GAGTACTTC-TAAGGTACA-CGTTATCCG
seq0009        TGGTGTCCGTGGAGGGGGTGT----------GAGTACTTCGTAAGGTACAGCGTTCTCCG
seq0013        GGGAGTCGAGCGAG---TTGTCAAC--AGTAAAATACTTC-TAGGATACAACGGTTCCGT
seq0014        GGGAGTCCGTGGAGGAATTGTCAAC--AGACAATTACTTC-TAAGGTACGAGGGTTACCG
seq0015        ------------------------------------------------------------
seq0018        GGGAGTCTGATGTCAACCGTC------GTCTACTAATCTC-TACGGTACGGC--GCTGCG
seq0020        GAGAGTCTGTGGAGGAGTGGCCAACTACACTGCTAACCTC-TAAGCTGC-----GTTTTG

(position)     66666666667777777777
               01234567890123456789
                                   
seq0000        AAACAAAGGATATCCGCAGA
seq0001        AAACAAAGAATATCCGCAGA
seq0002        AAACAACGGATATCTGCAGA
seq0003        AAACAACGGATATCTGCAGA
seq0004        AAACAACGGATATCTGCAGA
seq0005        AAACAAAGGATATCCGCCGA
seq0006        AAACAAAGGATATCCGCCGA
seq0007        AAACAAAGGATATCCGCCGA
seq0008        ATACAAAGGGAATCCGCAGA
seq0009        ATACAAAGGGCATCCGCAGA
seq0013        GAGACACGGATATCCGGAGT
seq0014        ATACAAAGGTTAGCCGCAAA
seq0015        --------------------
seq0018        AAACAAGTGATAGCCGCAGA
seq0020        ATACAAAGG--AGCCCCACA


<<<<< 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, -6) .

[ 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    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5    -   -5   -5   -5
seq0001   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5    -   -5   -5   -5
seq0002   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0003   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0004   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0005   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0006   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0007   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0008   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -5   -5    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0009   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0013   	    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -5   -5    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0014   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -5   -5    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0  -11  -11  -11  -11  -11  -11  -11  -11  -11  -11    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0020   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -4   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -   -5   -5   -5   -5   -8   -8   -8   -8    -



(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

seq0000   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0001   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0002   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0003   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0004   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0005   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0006   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0007   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0008   	    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0009   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0013   	   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0014   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	   -5   -5    -    -   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6
seq0020   	    -    -    -    -   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6    -    -   -4   -6   -6   -6   -6   -6   -6   -6   -6




[INFORMATION] The original $commoner_shift_flank = -6. 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   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0001   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0002   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0003   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0004   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0005   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0006   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0007   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1
seq0008   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5    5    1    1    -    1    1    1
seq0009   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5    5    1    1    1    1    1    1
seq0013   	    -    -    -    -    -    -    6    6    6    6    6    6    6    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3    3    3    3    -    -    5    5    5    5    5    5    5    5    5    5    5    1    1    -    1    1    1
seq0014   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    3    3    3    3    3    3    3    3    3    3    3    -    -    5    5    5    5    5    5    5    5    5    5    5    1    1    -    1    1    1
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    6    6   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1
seq0020   	    -    -    -    -    -    -    6    6    6    6    6    6    6    6    6    4    4    4    4    4    3    3    3    3    3    3    3    3    3    3    3    3    3    2    1    1    1    1    1    1    1    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

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



<<<<< 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 1 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} = 22) >>

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

0	6	14	29	21	6	n/a	0,1,2,3,4,5,6,7,8,9,11,14
1	6	12	20	23	6	n/a	10
2	6	16	26	22	6	n/a	13
3	13	19	20	3	0	n/a	10
4	15	19	29	18	4	n/a	0,1,2,3,4,5,6,7,8,9,11,14
5	17	26	26	0	-5	n/a	13
6	20	30	21	16	3	n/a	11
7	20	32	28	14	3	n/a	14
8	20	26	18	15	3	n/a	8,9
9	23	30	20	17	3	n/a	10
10	33	43	22	19	5	n/a	10,11
11	33	57	26	6	1	n/a	13
12	33	33	28	11	2	n/a	14
13	34	50	28	5	1	n/a	14
14	37	72	18	20,7	5,1	0	8,9
15	44	60	20	10	1	n/a	10
16	44	72	21	9	1	n/a	11
17	47	72	15	8	1	n/a	0,1,2,3,4,5,6,7
18	51	54	28	1	-2	n/a	14
19	60	63	29	13	3	n/a	13,14
20	64	72	29	4	1	n/a	13,14
21	77	77	28	12	2	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} = 22) >>>>>


[[ 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	0
2	2	0	0	0	0	0
3	2	1	0	0	0	0
4
5	1	1	1	0	0	0
6	0	0	1	1	0	0
7	1	1	0	0	0	0
8	0	0	2	2	0	0
9	0	1	0	0	0	0
10	0	0	0	0	0	0
11	0	0	1	3	0	0
12	2	1	0	0	0	0
13	2	0	0	0	0	0
14	0	0	1	1	0	0
15	1	0	0	0	0	0
16	0	0	1	0	0	0
17	1	1	0	0	0	0
18	1	1	0	0	0	0
19	1	1	0	0	0	0
20	1	0	0	0	0	0
21	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 0, 4, 10 . ]


[ 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	7	7	Complex(???)	20:7:12:X	None
2	0	11	11	Complex(???)	26:11:21:X/26:9:10:-	None
3	0	7	7	Merge(complementary)(+shift^2)(?)	20:7:12:X/20:16:16:-	20:20:22:X
4	Skipped!!(NO_RELEVANT_BRANCH)
5	0	10	10	Complex(???)	26:11:21:X/27:32:32:-	26:27:30:X
6	0	11	11	Complex(???)	20:16:16:-	20:20:22:X
7	0	13	13	Complex(???)	27:30:30:-	28:31:32:-
8	0	7	7	Complex(???)	19:24:31:X/15:17:44:X	19:27:36:X/15:20:45:X
9	0	8	8	Complex(???)	None	20:20:22:X
10	Skipped!!(NO_ASSOCIATED_EVENT(???))
11	0	25	25	Complex	27:32:32:-	28:31:32:-/25:58:59:-/27:55:57:-
12	0	1	1	Complex(???)	27:30:30:-/27:32:32:-	28:31:32:-
13	0	17	17	Complex(???)	27:32:32:-/27:50:52:-	None
14	0	40	36	Complex(???)	19:24:31:X	19:27:36:X
15	0	17	17	Complex(???)	20:60:60:X	None
16	0	29	29	NO_ASSOCIATED_EVENT(???)	20:72:72:-	None
17	0	26	26	Shift(???)	15:17:44:X	15:20:45:X
18	0	4	4	Shift	27:50:52:-	27:55:57:-
19	0	4	4	Shift	25:61:62:-	25:58:59:-
20	0	9	9	Complex(???)	25:61:62:-	None
21	0	1	1	Shift	27:76:77:-	27:75:76:-


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:85	{Equivalent to '23:6:85'(rec)}
20:7:12	1,3
26:9:10	2
26:11:21	2,5
20:16:16	3,6
15:17:44	8,17
19:24:31	8,14
27:30:30	7,12
27:32:32	5,11,12,13
25:39:42	None
17:45:45	{Equivalent to '17:46:46'(rec)}
27:50:52	13,18
3:51:51	{Equivalent to '3:52:52'(rec)}
16:55:55	{Equivalent to '16:56:56'(rec)}
20:60:60	15
25:61:62	19,20
20:72:72	16
27:76:77	21


[ Contents of %indel_rec2assoc_cblks ]

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

23:6:85	{Equivalent to '23:0:85'(ref)}
20:20:22	3,6,9
15:20:45	8,17
26:27:30	5
19:27:36	8,14
28:31:32	7,11,12
17:46:46	{Equivalent to '17:45:45'(ref)}
3:52:52	{Equivalent to '3:51:51'(ref)}
27:55:57	11,18
16:56:56	{Equivalent to '16:55:55'(ref)}
25:58:59	11,19
27:75:76	21


<<<< (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} = 2) ]

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

0	=> [2],
9	=> [6],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

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

2	=> [0],
6	=> [9],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 3) ]

Indx_cblk_A	indx_cblk_B

3	6
3	1
19	20


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

[ For the 1 th pair: (3, 6) ]

[ For the 2 th pair: (3, 1) ]

[ For the 3 th pair: (19, 20) ]

