<<<<< 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 = 83 .


<< 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        GGAAGTCTGCGG-----------------------------CTTACGG-ACAGCGTTCTC
seq0001        GGAAGTCTGCGG-----------------------------CTTACGG-ACAGCGTTCTC
seq0002        GGCAGTCTGCGT-----------------------------CTTAGGGTACAGCGTTCTC
seq0003        GGCAGTCTGCGG-----------------------------CTTAGGGTACAGCGTTCTC
seq0004        GGCAGTCTGCGG-----------------------------CTTAGGGTACAGCGTTCTC
seq0005        GGAAGTCTGCGG-----------------------------CTTAGGGAACAGCGTTCTC
seq0006        GGAAGTCTGTGG-----------------------------CTTAGGGTACAGCGTTCTC
seq0007        GGAAGTCTGCGC-----------------------------CTTAGGGTACAGCGTTCTC
seq0008        GGGAGTCCGTAGAGGGGTTGTG--------AGTACT----TC-TAAGGTACA-CGTTATC
seq0009        TGGTGTCCGTGGAGGGGGTGTG--------AGTACT----TCGTAAGGTACAGCGTTCTC
seq0013        GGGAGTCGAGCGAG---TTGTCAACAGTAAAATACT----TC-TAGGATACAACGGTTCC
seq0014        GGGAGTCCGTGGAGGAATTGTCAACAGACAATTACT----TC-TAAGGTACGAGGGTTAC
seq0015        ------------------------------------------------------------
seq0018        GGGAGTCTGA--------TGTCAACCGTCGTCTACTAATCTC-TACGGTACGGCG--CTG
seq0020        GAGAGTCTGTGGAGGAGTGGCCAAC--TACACTGCTAACCTC-TAAG---CTGCG--TTT

(position)     66666666667777777777888
               01234567890123456789012
                                      
seq0000        -CGAAACAAAGGATATCCGCAGA
seq0001        -CGAAACAAAGAATATCCGCAGA
seq0002        -CGAAACAACGGATATCTGCAGA
seq0003        -CGAAACAACGGATATCTGCAGA
seq0004        -CGAAACAACGGATATCTGCAGA
seq0005        -TAAAACAAAGGATATCCGCCGA
seq0006        -CAAAACAAAGGATATCCGCCGA
seq0007        -CGAAACAAAGGATATCCGCCGA
seq0008        -CGATACAAAGGGAATCCGCAGA
seq0009        -CGATACAAAGGGCATCCGCAGA
seq0013        GTGAGACAC-GGATATCCGGAGT
seq0014        -CGATACAAAGGTTAGCCGCAAA
seq0015        -----------------------
seq0018        -CGAAACAAGTGATAGCCGCAGA
seq0020        -TGATACAAAGG--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, -3) .

[ 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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3    -   -3
seq0001   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3    -   -3
seq0002   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0003   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0004   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0005   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0006   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0007   	    0    0    0    0    0    0    0    0    0   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   -3   -3   -3   -3   -3   -3   -3
seq0008   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3  -11    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -    -   -3   -3    -   -3   -3   -3   -3   -3   -3   -3
seq0009   	    0    0    0    0    0    0    0    0    0   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3  -11    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0013   	    0    0    0    0    0    0    0   -6   -6   -6   -6   -6   -6   -6    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -   -3   -3    -   -3   -3   -3   -3   -3   -3   -3
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   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -   -3   -3    -   -3   -3   -3   -3   -3   -3   -3
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    8   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -3   -3   -3   -3   -3   -3   -3
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    -    -   -1   -1   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -3   -3   -3   -3    -    -    -



(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

seq0000   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0001   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0002   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0003   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0004   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0005   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0006   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0007   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0008   	   -3   -3    -   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0009   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0013   	   -3   -3   -3   -3   -3   -3   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0014   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	   -3   -3   -3   -3   -3    -    -   -1   -1   -1    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0020   	   -3   -3   -3   -3   -3    -    -   -1   -1   -1    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3    -    -   -1   -3   -3   -3   -3   -3   -3   -3   -3




[INFORMATION] The original $commoner_shift_flank = -3. 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   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0001   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0005   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0006   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0007   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   30    0    0    0    0
seq0008   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    -    0    0    0    0
seq0009   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0   -8    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    0    0    0    0    0    0    0
seq0013   	    -    -    -    3    3    3    3    3    3    3   -3   -3   -3   -3   -3   -3   -3    -    -    -    0    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   	    -    -    -    3    3    3    3    3    3    3    3    3    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    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    3    3    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -   11    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0
seq0020   	    -    -    -    3    3    3    3    3    3    3    3    3    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    -    -    2    2    1    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0



(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   	    0    -    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    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    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0   -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
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    -    2    2    2    -    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    0    0    0    0    0    -    -    2    2    2    -    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... >>>>>

... 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} = 23) >>

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

0	3	11	29	19	3	n/a	0,1,2,3,4,5,6,7,8,9,11,14
1	3	9	20	21	3	n/a	10
2	3	12	26	20	3	n/a	13
3	10	16	20	1	-3	n/a	10
4	12	14	15	15	1	n/a	0,1,2,3,4,5,6,7
5	12	16	29	13	1	n/a	8,9,11,14
6	17	62	21	10	0	n/a	11
7	17	27	28	3	0	n/a	14
8	17	23	18	7	0	n/a	8,9
9	20	59	20	11	0	n/a	10
10	21	21	26	22	11	n/a	13
11	22	57	26	6	0	n/a	13
12	24	24	18	0	-8	n/a	8,9
13	30	31	28	17	2	n/a	14
14	32	32	28	14	1	n/a	14
15	33	57	28	4	0	n/a	14
16	33	62	18	8	0	n/a	8,9
17	44	45	15	23	30	n/a	0,1,2,3,4,5,6,7
18	46	62	15	9	0	n/a	0,1,2,3,4,5,6,7
19	60	71	20	2	-1	n/a	10
20	60	62	29	16	2	n/a	13,14
21	64	72	29	12	1	n/a	0,1,2,3,4,5,6,7,8,9,11,13,14
22	77	77	28	18	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} = 23) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 3): 0, 5, 21 . ]


[ 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	10	10	Complex(???)	26:9:10:-	26:13:20:X
3	0	7	7	Merge(complementary)(+shift^2)(?)	20:7:12:X/20:16:16:-	20:17:19:X
4	0	3	3	Complex(???)	None	15:15:43:X
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	46	46	Complex	20:16:16:-	20:63:63:-/20:17:19:X
7	0	11	11	Complex(???)	None	27:28:29:-
8	0	7	7	Complex	19:24:31:X/15:17:44:X	None
9	0	40	40	Complex(???)	20:60:60:X	20:17:19:X
10	0	1	1	Merge(complementary)(+shift^2)(?)	26:11:21:X/26:9:10:-	26:13:20:X
11	0	36	36	Complex(???)	26:11:21:X	25:58:59:-
12	0	1	1	Shift(gap-aligned)(?)	19:24:31:X	19:25:32:X
13	0	2	2	Complex(???)	27:30:30:-	27:28:29:-
14	0	1	1	Complex(???)	27:30:30:-/27:32:32:-	None
15	0	25	25	Complex(???)	27:32:32:-	25:58:59:-
16	0	30	30	NO_ASSOCIATED_EVENT(???)	None	19:25:32:X
17	0	2	2	Inter-branch-transfer(rec>ref)(??)	15:17:44:X	15:15:43:X/19:45:45:-
18	0	17	17	Complex(???)	15:17:44:X	19:45:45:-
19	0	12	12	Overshoot-Merge(??)	20:60:60:X/20:72:72:-	20:72:72:X/20:63:63:-
20	0	3	3	Shift	25:61:62:-	25:58:59:-
21	Skipped!!(NO_RELEVANT_BRANCH)
22	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 '23:3:85'(rec)}
20:7:12	1,3
26:9:10	2,10
26:11:21	10,11
20:16:16	3,6
15:17:44	8,17,18
19:24:31	8,12
27:30:30	13,14
27:32:32	14,15
25:39:42	{Equivalent to '25:39:42'(rec)}
17:45:45	None
27:50:52	{Equivalent to '27:50:52'(rec)}
3:51:51	{Equivalent to '3:51:51'(rec)}
16:55:55	{Equivalent to '16:55:55'(rec)}
20:60:60	9,19
25:61:62	20
20:72:72	19
27:76:77	22


[ Contents of %indel_rec2assoc_cblks ]

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

23:3:85	{Equivalent to '23:0:85'(ref)}
26:13:20	2,10
15:15:43	4,17
20:17:19	3,6,9
19:25:32	12,16
27:28:29	7,13
25:39:42	{Equivalent to '25:39:42'(ref)}
19:45:45	17,18
16:45:45	None
27:50:52	{Equivalent to '27:50:52'(ref)}
3:51:51	{Equivalent to '3:51:51'(ref)}
16:55:55	{Equivalent to '16:55:55'(ref)}
25:58:59	11,15,20
20:63:63	6,19
20:72:72	19
27:75:76	22


<<<< (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]

0	=> [2],


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

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

2	=> [0],


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

Indx_cblk_A	indx_cblk_B

3	1
10	2
17	4


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

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


{ The representative path is: 1  -> 3 }


( 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)	3	9	3	3	20	10	10
2nd(reconstructed)	10	16	-3	-3	20	10	10


( 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)	Complex(???)	20:7:12:X	20:10:12:X
2nd(reconstructed)	Shift	20:10:12:X	20:17:19:X


[ For the 2 th pair: (10, 2) ]


{ The representative path is: 2  -> 10 }


( 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)	3	13	3	3	26	0,1,2,3,4,5,6,7,8,9,11,13,14	13
2nd(reconstructed)	21	21	8	8	26	13	13


( 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)	Merge(complementary)	26:11:21:X/26:9:10:-	26:14:21:X
2nd(reconstructed)	Shift	26:14:21:X	26:13:20:X


[ For the 3 th pair: (17, 4) ]

