<<<<< 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 = 81 ,
#{Sites in the segment}_rec = 100 .


<< 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        A---CAGCCAAAATC-GGCTTTA----AC-------------------------------
seq0001        A---CAGCCAAAATC-GGCTTTA----AC-------------------------------
seq0002        A---CAGCCAAAATC-GGCTTTA----AC-------------------------------
seq0003        A---CAGCCAAAATC-GGCTTTA----AC-------------------------------
seq0004        A---CAGCCAAAATC-GGCTTTA----AC-------------------------------
seq0005        A---CAGCCAGAATC-GTCTTTA----AC-------------------------------
seq0006        A---CAGCCAGAATC-GTCTTTACATAAC-------------------------------
seq0007        A---CAGCCAGAATC-GTCTTTACATAAC-------------------------------
seq0008        C---CAGTCAAAATC-GTCTTTA----AG-------------------------------
seq0009        A---GAGCCCAAATC-G-------------------------------------------
seq0013        G-------GAA-A-C-GTCCTTG----AGCCGGTTGGAAAGAAATATACGTTCCTCATCA
seq0014        ------------------------------------------------------------
seq0015        A-------CT-AA-T-GTCCTTA----AT-------------------------------
seq0018        AATTCAGCCAAA--CGGTCTTCA----AG-------------------------------
seq0020        T---TAGCCAAA------------------------------------------------

(position)     666666666677777777778
               012345678901234567890
                                    
seq0000        -------GCCTATCTCTT-AT
seq0001        -------GCCTATCTCTT-AT
seq0002        -------CCCTATCTCTT-AT
seq0003        -------GCCTATCTCTT-AT
seq0004        -------GCCTATCTCTT-AT
seq0005        -------GCCTATCCCTT-AT
seq0006        -------GCCTATCTCTT-AT
seq0007        -------GCCAATCTCTT-AT
seq0008        -------CCCTATCCATTCGA
seq0009        --------CCCATCCATT-AT
seq0013        AATGATCGCCTTTT-ATT-AT
seq0014        ----------TTTAC----AT
seq0015        -------GCCTTTACACT-AT
seq0018        -------GCCTACACATT-AT
seq0020        -------------ACAAA-AT


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---------------------------------------------------------A--
seq0001        ---------------------------------------------------------A--
seq0002        ---------------------------------------------------------A--
seq0003        ---------------------------------------------------------A--
seq0004        ---------------------------------------------------------A--
seq0005        ---------------------------------------------------------A--
seq0006        ---------------------------------------------------------A--
seq0007        ---------------------------------------------------------A--
seq0008        ---------------------------------------------------------C--
seq0009        ---------------------------------------------------------A--
seq0013        GGAAACGTCCTTGAGCCGGTTGGAAAGAAATATACGTTCCTCATCAAATGATCGCCT---
seq0014        ------------------------------------------------------------
seq0015        ---------------------------------------------------------A--
seq0018        ---------------------------------------------------------AAT
seq0020        ---------------------------------------------------------T--

(position)     6666666666777777777788888888889999999999
               0123456789012345678901234567890123456789
                                                       
seq0000        -CAGCCAAAATCGGCTT----TAACGCCTATC-TCTTAT-
seq0001        -CAGCCAAAATCGGCTT----TAACGCCTATC-TCTTAT-
seq0002        -CAGCCAAAATCGGCTT----TAACCCCTATC-TCTTAT-
seq0003        -CAGCCAAAATCGGCTT----TAACGCCTATC-TCTTAT-
seq0004        -CAGCCAAAATCGGCTT----TAACGCCTATC-TCTTAT-
seq0005        -CAGCCAGAATCGTCTT----TAACGCCTATC-CCTTAT-
seq0006        -CAGCCAGAATCGTCTTTACATAACGCCTATC-TCTTAT-
seq0007        -CAGCCAGAATCGTCTTTACATAACGCCAATC-TCTTAT-
seq0008        -CAGTCAAAATCGTCTT----TAAGCCCTATC-CATTCGA
seq0009        -GAGCCCAAATCG-------------CCCATC-CATTAT-
seq0013        ----------------------------TTTATT---AT-
seq0014        ----------------------------TTTA-C---AT-
seq0015        -CT------AATGTCCT----TAATGCCTTTA-CACTAT-
seq0018        TCAGCC-AAACGGTCTT----CAAGGCCTACA-CATTAT-
seq0020        -TAGCC-AAA---------------------A-CAAAAT-


<<<<< 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, 19) .

[ 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0   -7   -7   -7   -8   -9  -10  -10  -10  -10  -10  -10  -10  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0001   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0002   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0003   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0004   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0005   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0006   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56   56   56   56   56   56   56   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0007   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56   56   56   56   56   56   56   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0008   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   19   19   19
seq0009   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57   57   57   57   57   57   57   56    -    -    -    -    -    -    -    -    -    -    -    -    -   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0013   	  -14  -14  -14  -14  -14  -14  -14    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   17   16   16   16    -    -    -   18   18    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   18   18   18   18    -   19    -    -    -   18   18    -
seq0015   	    -    -    -    -    -    -    -   57    -    -    -   53   53    -    -    -    -    -    -   58   58   57   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0018   	    -    -    -    -    -    -    -   57   57   57   57   57   57   57   57   57    -   58   58   58   56   56   56   56   56   56   56    -    -    -    -   60   60   56   56   18   18   18   18   18   18   18    -   19   19   19   19   18   18    -
seq0020   	    -    -    -    -    -    -    -   57    -    -    -   57   57   57   57   57    -   58   58   58    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   18    -   19   19   19   19   18   18    -




[INFORMATION] The original $commoner_shift_flank = 19. Thus, we will shift the entire reference 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	  -19  -26  -26  -26  -27  -28  -29  -29  -29  -29  -29  -29  -29  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33  -33
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0001   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0002   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0003   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0004   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0005   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0006   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37   37   37   37   37   37   37   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0007   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37   37   37   37   37   37   37   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0008   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38   38   38   38   38   38   38   37    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0013   	  -33  -33  -33  -33  -33  -33  -33    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2   -3   -3   -3    -    -    -   -1   -1    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1    -    0    -    -    -   -1   -1    -
seq0015   	    -    -    -    -    -    -    -   38    -    -    -   34   34    -    -    -    -    -    -   39   39   38   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0018   	    -    -    -    -    -    -    -   38   38   38   38   38   38   38   38   38    -   39   39   39   37   37   37   37   37   37   37    -    -    -    -   41   41   37   37   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0   -1   -1    -
seq0020   	    -    -    -    -    -    -    -   38    -    -    -   38   38   38   38   38    -   39   39   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1    -    0    0    0    0   -1   -1    -



<<<<< 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} = 20) >>

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

0	0	0	20	5	-19	n/a	10
1	1	56	20	4,3,2,1,0	-26,-27,-28,-29,-33	0,0,0,0	10
2	57	71	19	22	38	n/a	0,1,2,3,4,5,6,7,8,9
3	57	57	23	23	38	n/a	12
4	57	69	29	21,25	38,39	0	13,14
5	61	62	23	15	34	n/a	12
6	69	71	23	26,24	39,38	0	12
7	70	76	26	18	37	n/a	13
8	72	76	25	17	37	n/a	0,1,2,3,4,5,8,12
9	72	84	13	20	37	n/a	6,7
10	72	72	17	19	37	n/a	9
11	81	82	27	27	41	n/a	0,1,2,3,4,5,8,12,13
12	83	84	27	16	37	n/a	0,1,2,3,4,5,8,12,13
13	85	91	27	9	-1	n/a	0,1,2,3,4,5,6,7,8,12,13
14	86	91	17	12	-1	n/a	9
15	88	90	20	7	-2	n/a	10
16	88	91	21	11	-1	n/a	11
17	91	93	20	6	-3	n/a	10
18	91	91	28	10	-1	n/a	14
19	97	98	29	8	-1	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13,14



<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<< (1) For Reference MSA >>>

<<< (2) For Reconstructed MSA >>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 20) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 5): 8, 10, 11, 12, 14 . ]


[ Contents of @cblk_wise_msa_errors ]

Indx_cmp_blk	Indx_error	len_cblk_ref	len_cblk_rec	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(ref)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(rec)

0	0	1	1	Complex(???)	21:19:88:X	20:0:56:-
1	0	63	56	Complex(???)	20:48:85:-	20:0:56:-/22:57:87:X
2	0	15	15	Shift(???)	19:32:32:-	19:66:66:-
3	0	1	1	Complex(???)	24:23:26:X	22:57:87:X
4	0	12	13	Complex(???)	25:31:31:-	27:70:90:-
5	0	2	2	Complex(???)	23:29:29:X/24:23:26:X	24:63:68:X
6	0	4	3	Complex(???)	23:29:29:X/22:30:30:X	24:63:68:X
7	0	7	7	Complex	26:34:34:-/25:31:31:-/27:33:91:-	27:70:90:-
8	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
9	0	13	13	Shift(???)	13:42:45:-	13:77:80:-
10	Skipped!!(NO_ASSOCIATED_EVENT(???))
11	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
12	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
13	0	7	7	Complex(???)	20:48:85:-/20:93:93:X	22:57:87:X/20:92:92:-
14	Skipped!!(NO_ASSOCIATED_EVENT(???))
15	0	3	3	Complex(???)	20:93:93:X	22:57:87:X
16	0	4	4	Complex(???)	21:19:88:X/20:93:93:X	22:57:87:X/20:92:92:-
17	0	3	3	Complex(???)	20:93:93:X/21:94:96:X	20:92:92:-/22:94:96:X
18	0	1	1	Complex(???)	27:33:91:-	27:70:90:-
19	0	2	2	Shift	16:97:97:-	16:99:99:-


[ Contents of %indel_ref2assoc_cblks ]

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

21:19:88	0,16
26:20:22	{Equivalent to '26:58:60'(rec)}
24:23:26	3,5
23:29:29	5,6
22:30:30	6
25:31:31	4,7
19:32:32	2
27:33:91	7,18
26:34:34	7
17:36:86	{Equivalent to '17:73:85'(rec)}
13:42:45	9
20:48:85	1,13
20:93:93	13,15,16,17
21:94:96	17
16:97:97	19


[ Contents of %indel_rec2assoc_cblks ]

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

20:0:56	0,1
22:57:87	1,3,13,15,16
26:58:60	{Equivalent to '26:20:22'(ref)}
24:63:68	5,6
19:66:66	2
27:70:90	4,7,18
17:73:85	{Equivalent to '17:36:86'(ref)}
13:77:80	9
20:92:92	13,16,17
22:94:96	17
16:99:99	19


<<<< (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]

8	=> [7,9],
12	=> [9],
14	=> [13],


[ Contents of %cb2hard_linking (#{keys} = 3) ]

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

7	=> [8],
9	=> [8,12],
13	=> [14],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

