<<<<< 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 = 108 ,
#{Sites in the segment}_rec = 107 .


<< 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        -------AGT--AA------AT-AGGATCTCA--AGCACTA-------------------
seq0001        -------AGT--AA------AT-AGGATCTCA--AGCACTA-------------------
seq0002        -------AGT--AA------AT-TGGATCTTA--AGCACTAAGTCGATGGTCATACATGG
seq0003        -------AGT--AA------AT-AGGATCTCA--AGCACTAAGTCGATGGTCGTACATGG
seq0004        -------AGT--AA------AT-AGGATCTCA--AGCACTAAGTCGATGGTCGTACATGG
seq0005        -------AGT--AA------ATGAGGATTTCA--AGCACTA-------------------
seq0006        -------AGT--AA------ATGAGGATCTCA--AGCACTA-------------------
seq0007        -------AGT--AA------ATGAGGATCTCA--AGCACGA-------------------
seq0008        -------AGT--AA------ATGAGGATCAAA--ACAACTA-------------------
seq0009        -------AGT-AAA------A---GCATCTAA--ATAACTA-------------------
seq0013        -------CTT--AAAGCG------------------------------------------
seq0014        GTGAGTAAGT--AAAGCAGCATGAGGATCTAA--GTAACTA-------------------
seq0015        -------AGT--AACTCGGAATGAGGCTGTCA--ACAGCCA-------------------
seq0018        -------CGT---AAGCGGAATGTGGATCTACCGATGACTA-------------------
seq0020        -------CCTT-AAAGCGTAATGCGGATATAA--ATAACTA-------------------

(position)     000000000000000000000000000000000000000011111111
               666666666677777777778888888888999999999900000000
               012345678901234567890123456789012345678901234567
                                                               
seq0000        ------------CATACT-------------AAGGTGAAGTCTCCTCT
seq0001        ------------CATACT-------------AAGGTGAAGTCTCCTCT
seq0002        CAAAACCCCTTACATACT-------------AAGGTGAAGTCTCTTCT
seq0003        CAAAACCCCTTACATACT-------------AAGGTCAAGTCTCTTCT
seq0004        CAAAACCCCTTACATACT-------------AAGGTGAAGTCTCTTCT
seq0005        ------------CATACC-------------AAAGTGAAGTCTCCTCT
seq0006        ------------CATACCGGTACAGCGGGATAAAGTGAAGTCTCCTCT
seq0007        ------------CATACCGG--CAGCGGGATAAAGTGAAGTCTCATCT
seq0008        ------------CATACA-------------AAGGTGAAGTCTCCTAT
seq0009        ------------TATCCA-------------AAGGTGAAGTCTCCCAT
seq0013        -----------------------------------------AACTT--
seq0014        ------------CAGACC-------------AAGGTGAAGTCACCTCA
seq0015        ------------TAGACC-------------AAGTAGAAGTCACCTGT
seq0018        ------------CAGACC-------------CAGAAGAAGTCACCTCT
seq0020        ------------CAGCCC-------------CCGGAGGAGGCAGCCCC


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -AG-------TAA------AT-AGGATCTCA--AGCACT---------------------
seq0001        -AG-------TAA------AT-AGGATCTCA--AGCACT---------------------
seq0002        -AG-------TAA------AT-TGGATCTTA--AGCACTAAGTCGATGGTCATACATGGC
seq0003        -AG-------TAA------AT-AGGATCTCA--AGCACTAAGTCGATGGTCGTACATGGC
seq0004        -AG-------TAA------AT-AGGATCTCA--AGCACTAAGTCGATGGTCGTACATGGC
seq0005        -AG-------TAA------ATGAGGATTTCA--AGCACT---------------------
seq0006        -AG-------TAA------ATGAGGATCTCA--AGCACT---------------------
seq0007        -AG-------TAA------ATGAGGATCTCA--AGCACG---------------------
seq0008        -AG-------TAA------ATGAGGATCAAA--ACAACT---------------------
seq0009        -AG-------TAA------A--AGCATCTAA--ATAACT---------------------
seq0013        -CT-------TAAAGC--------GAACT-------------------------------
seq0014        -GTGAGTAAGTAAAGCAGCATGAGGATCTAA--GTAACT---------------------
seq0015        -AG-------TAACTCGGAATGAGGCTGTCA--ACAGCC---------------------
seq0018        -CG-------TAA-GCGGAATGTGGATCTACCGATGACT---------------------
seq0020        CCT-------TAAAGCGTAATGCGGATATAA--ATAACT---------------------

(position)     00000000000000000000000000000000000000001111111
               66666666667777777777888888888899999999990000000
               01234567890123456789012345678901234567890123456
                                                              
seq0000        ----------ACATACT-------------AAGGTGAAGTCTCCTCT
seq0001        ----------ACATACT-------------AAGGTGAAGTCTCCTCT
seq0002        AAAACCCCTTACATACT-------------AAGGTGAAGTCTCTTCT
seq0003        AAAACCCCTTACATACT-------------AAGGTCAAGTCTCTTCT
seq0004        AAAACCCCTTACATACT-------------AAGGTGAAGTCTCTTCT
seq0005        ----------ACATACC-------------AAAGTGAAGTCTCCTCT
seq0006        ----------ACATACCGGTACAGCGGGATAAAGTGAAGTCTCCTCT
seq0007        ----------ACATACCGG--CAGCGGGATAAAGTGAAGTCTCATCT
seq0008        ----------ACATACA-------------AAGGTGAAGTCTCCTAT
seq0009        ----------ATATCCA-------------AAGGTGAAGTCTCCCAT
seq0013        ----------------------------------------------T
seq0014        ----------ACAGACC-------------AAGGTGAAGTCACCTCA
seq0015        ----------ATAGACC-------------AAGTAGAAGTCACCTGT
seq0018        ----------ACAGACC-------------CAGAAGAAGTCACCTCT
seq0020        ----------ACAGCCC-------------CCGGAGGAGGCAGCCCC


<<<<< 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, -1) .

[ 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    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0003   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0004   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0005   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -   -6   -6    -    -    -    -    -    -    -    1    0    0    -    -    -    -    -    -    6    -    -    2   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    7  -76  -76  -76  -76    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    1    1    1    1    1    1    1    1    1    1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -   -6   -6    -    -    -    -    -    -    -    1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -   -6   -6    -    -    -    -    -    -    -    1   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -7   -7   -7    -    -    -    -    -    -    -    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0002   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0003   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0004   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1



(position)	  100  101  102  103  104  105  106

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




[INFORMATION] The original $commoner_shift_flank = -1. 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   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    -    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    -    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -   -5   -5    -    -    -    -    -    -    -    2    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    0
seq0003   	    -    -   -5   -5    -    -    -    -    -    -    -    2    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    0
seq0004   	    -    -   -5   -5    -    -    -    -    -    -    -    2    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    0
seq0005   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -   -5   -5    -    -    -    -    -    -    -    2    1    1    -    -    -    -    -    -    7    -    -    3    0    0    0    0    0    0    0    0    -    -    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -   -5   -5    -    -    -    -    -    -    -    2    0    0    0    0    0    -    -    -    -    -    -    -    -    8  -75  -75  -75  -75    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    2    2    2    2    2    2    2    2    2    2    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   	    -    -   -5   -5    -    -    -    -    -    -    -    2    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    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -   -5   -5    -    -    -    -    -    -    -    2   -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    -    -    -    -    -    -    -    -    -    -
seq0020   	    -   -6   -6   -6    -    -    -    -    -    -    -    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    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    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    0    0    0    0    0    0    0    0    0    0    0    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    0    0    0    0    0    0    0    0    0    0    0    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    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    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
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    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
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   31    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0



(position)	  100  101  102  103  104  105  106  107

seq0000   	    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    2
seq0014   	    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0
seq0020   	    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} = 12) >>

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

0	1	11	28	1,8	-6,1	0	14
1	2	3	27	2	-5	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
2	2	11	21	11	2	n/a	11
3	11	11	27	10	2	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
4	12	13	26	3	-1	n/a	13
5	12	13	17	9	1	n/a	9
6	20	20	17	14	7	n/a	9
7	23	23	17	13	3	n/a	9
8	25	25	20	15	8	n/a	10
9	26	29	20	0	-75	n/a	10
10	71	71	29	16	31	n/a	0,1,5,6,7,8,9,11,12,13,14
11	107	107	20	12	2	n/a	10



<<<<< 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} = 12) >>>>>


[[ 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	1	0	0	0
1
2	1	1	0	0	0	0
3
4	1	1	0	0	0	0
5	1	0	0	0	0	0
6	0	1	0	0	0	0
7	1	1	0	0	0	0
8	1	1	0	0	0	0
9	1	1	0	0	0	0
10	1	1	0	0	0	0
11	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 2): 1, 3 . ]


[ 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	4	11	Complex(???)	28:10:10:-/26:12:12:X	28:1:1:-
1	Skipped!!(NO_RELEVANT_BRANCH)
2	0	10	10	Shift(???)	21:0:6:-	21:4:10:-
3	Skipped!!(NO_RELEVANT_BRANCH)
4	0	2	2	Shift	26:12:12:X	26:14:14:X
5	0	2	2	Complex(???)	17:11:11:-	None
6	0	1	1	Complex(???)	None	17:21:22:X
7	0	1	1	Complex(???)	17:21:23:X	17:21:22:X
8	0	1	1	Complex(???)	20:18:100:X	20:17:24:X
9	0	4	4	Complex(???)	20:18:100:X	20:30:106:X
10	0	1	1	Shift	8:41:71:-	8:40:70:-
11	0	1	1	Complex(???)	20:106:107:X	20:30:106:X


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:6	2
28:10:10	0
17:11:11	5
26:12:12	0,4
19:14:19	None
20:18:100	8,9
17:21:23	7
9:22:22	None
26:32:33	{Equivalent to '26:32:33'(rec)}
8:41:71	10
13:78:90	{Equivalent to '13:78:90'(rec)}
11:80:81	{Equivalent to '11:80:81'(rec)}
20:106:107	11


[ Contents of %indel_rec2assoc_cblks ]

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

28:1:1	0
21:4:10	2
26:14:14	4
19:14:19	None
20:17:24	8
17:21:22	6,7
9:22:22	None
20:30:106	9,11
26:32:33	{Equivalent to '26:32:33'(ref)}
8:40:70	10
13:78:90	{Equivalent to '13:78:90'(ref)}
11:80:81	{Equivalent to '11:80:81'(ref)}


<<<< (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]

3	=> [2],


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

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

2	=> [3],


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

Indx_cblk_A	indx_cblk_B

4	0
6	7


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

[ For the 1 th pair: (4, 0) ]

[ For the 2 th pair: (6, 7) ]

