<<<<< 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 = 192 ,
#{Sites in the segment}_rec = 190 .


<< 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        ACC----ACG-------------TAGTCATCGGTCTTGCCAGCCGAGTTTGAAAC-GTC-
seq0001        ACC----ACG-------------TAGACATCGGTCTTGCCAGCCGAGTTTGAAAC-GTC-
seq0002        ATC----ACG-------------TAGTCATCGGTCTTGCCAGCCCAGTCTGACAC-GTC-
seq0003        ACC----ACG-------------TAATCATCGGTCTTGCCAGCC-AGTCTGACAC-GTC-
seq0004        ACC----ACG-------------TAGTCATCGGTCTTGCCAGCCCAGTCTGACAG-GTC-
seq0005        ACC----ACG-------------TATTCAGCGGTCTTGCCAGCCCAGTCTGAAAC-TTC-
seq0006        GCC----ACG-------------TAATCATCGGTCTTGCCAGCCCAGTCTGAAAC-TTC-
seq0007        ACC----ACG-------------TATTCATCGGTCTTGCCAGCCCAGTCTGAAAC-T---
seq0008        TGC----ATG-------------TTGTCATCGCTCTTGCCAGCCCAGCCTGAAACGGTC-
seq0009        TTG----ATG--------------------------------------------------
seq0013        ATC----ATG-------------TTATTATCG-TCATGCC-CCCCATCCAGCGAC-TAC-
seq0014        TTC----ATT-------------TTGTTATCGGTCTTGCCAGCCAGGACTG---C-GTC-
seq0015        TTC----ACC-------------TTGTT-TGGGTCTAGCCAGCCCAGCCCGAAAC-ATC-
seq0018        TTC----ACGCGCGAGACCATTTGTGTCATCGGTCTTGACCGCCCAACCTTAAAC-GTCT
seq0020        CTCGTACATGCGCGTAACCCTTTTTAGGATCGGTCATGACCACCCAT--ATAAAC-GTC-

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------------------------------------
seq0001        ------------------------------------------------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ------------------------------------------------------------
seq0014        ------------------------------------------------------------
seq0015        ------------------------------------------------------------
seq0018        CTGTTACGGTGGGGTGATGGGTCAGGATTTGCTACCCCGTAGAGACGATGAAGCGCTAAT
seq0020        ------------------------------------------------------------

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -------------------------CGGCGC-ATTAACTAGGCCACC-TGC--GATTCAG
seq0001        -------------------------CGGCGC-ATTAACTAGGCCACC-TGC--GATTCAG
seq0002        -------------------------CGGCGC-ATTAACTAGGCCACC-TGC--GATTCCG
seq0003        -------------------------CGGCAC-ATTAACTAGGCCACC-TGC--GATTCCG
seq0004        -------------------------CGGCGC-ATTAACTAGGCCACC-TGC--GATTCCG
seq0005        -------------------------GGGCGC-ATTAACTAGGCCACC-TGC--CATTCAG
seq0006        -------------------------GAGCGC-ATTAACTAGGCCACC-TGC--CATTCAG
seq0007        ----------------------------CGC-ATTGACTAGGCCACC-TGC--CATTCAG
seq0008        -------------------------GTGCGC-ATCAACGTG-GCACG-GGTCCGATTCAT
seq0009        --------------------------------------------------TCCGTTTCAA
seq0013        -------------------------CGGCGC-ATGAACTAGGCCACC-GCC--GGTTCGT
seq0014        -------------------------GTGCGC-ATGAACTAGGCCACC-GCC--TGCTCGT
seq0015        -------------------------GGGCGC-ATGAACTAGGCCACCCGCC--TCTTCGT
seq0018        TTCCCAATGGCACTTGATTGTAAAGGGGCGC-ATGAACTAGGCCACC-TAC--GGTTCAA
seq0020        -------------------------CGGCGCCATGAACTAGGCCACC-GGG--GGATTAT

(position)     111111111111
               888888888899
               012345678901
                           
seq0000        AGTCTGGGA-AC
seq0001        AGTCTGGGA-AC
seq0002        AGTCTGGGG-AC
seq0003        CGTCTGGGG-AC
seq0004        AGTCTGGGG-AC
seq0005        AGTCTGGTA-AC
seq0006        AGTCTGGTA-AC
seq0007        AGTCTGGTA-AC
seq0008        AGATTGGTA-AC
seq0009        --ACTGGTAAAC
seq0013        AGACTGGTC-AC
seq0014        -GACGGGTA-AC
seq0015        AGACTCGTT---
seq0018        AGACTGGTC-AC
seq0020        GGACTCGTA-AC


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ----ACCACGT-------------AGTCATCGGTCTTGCCAGCCGAGTTTGAAACG-TC-
seq0001        ----ACCACGT-------------AGACATCGGTCTTGCCAGCCGAGTTTGAAACG-TC-
seq0002        ----ATCACGT-------------AGTCATCGGTCTTGCCAGCCCAGTCTGACACG-TC-
seq0003        ----ACCACGT-------------AATCATCGGTCTTGCCAGCC-AGTCTGACACG-TC-
seq0004        ----ACCACGT-------------AGTCATCGGTCTTGCCAGCCCAGTCTGACAGG-TC-
seq0005        ----ACCACGT-------------ATTCAGCGGTCTTGCCAGCCCAGTCTGAAACT-TC-
seq0006        ----GCCACGT-------------AATCATCGGTCTTGCCAGCCCAGTCTGAAACT-TC-
seq0007        ----ACCACGT-------------ATTCATCGGTCTTGCCAGCCCAGTCTGAAACT----
seq0008        ----TGCATGT-------------TGTCATCGCTCTTGCCAGCCCAGCCTGAAACGGTC-
seq0009        ----T---TGA-------------TGTC--------------------------------
seq0013        ----ATCATGT-------------TATTATCG-TCATGCCCCC-CATCCAGCGACT-AC-
seq0014        ----TTCATTT-------------TGTTATCGGTCTTGCCAGC-CAG--GACTGCG-TC-
seq0015        ----TTCACCT-------------TGTT-TGGGTCTAGCCAGCCCAGCCCGAAACA-TC-
seq0018        ----TTCACGCGCGAGACCATTTGTGTCATCGGTCTTGACCGCCCAACCTTAAACG-TCT
seq0020        CTCGTACATGCGCGTAACCCTTTTTAGGATCGGTCATGACCACCCAT--ATAAACG-TC-

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------------------------------------
seq0001        ------------------------------------------------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ------------------------------------------------------------
seq0014        ------------------------------------------------------------
seq0015        ------------------------------------------------------------
seq0018        CTGTTACGGTGGGGTGATGGGTCAGGATTTGCTACCCCGTAGAGACGATGAAGCGCTAAT
seq0020        ------------------------------------------------------------

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -------------------------CGGCG-CATTAACTAGGC-CA-CCTGCGATTCAGA
seq0001        -------------------------CGGCG-CATTAACTAGGC-CA-CCTGCGATTCAGA
seq0002        -------------------------CGGCG-CATTAACTAGGC-CA-CCTGCGATTCCGA
seq0003        -------------------------CGGCA-CATTAACTAGGC-CA-CCTGCGATTCCGC
seq0004        -------------------------CGGCG-CATTAACTAGGC-CA-CCTGCGATTCCGA
seq0005        -------------------------GGGCG-CATTAACTAGGC-CA-CCTGCCATTCAGA
seq0006        -------------------------GAGCG-CATTAACTAGGC-CA-CCTGCCATTCAGA
seq0007        ----------------------------CG-CATTGACTAGGC-CA-CCTGCCATTCAGA
seq0008        -------------------------GTGCG-CATCAACGTGGCACG-GGTCCGATTCATA
seq0009        ----------------------------CG-TTTCAAACTGGTA----------------
seq0013        -------------------------CGGCG-CATGAACTAGGC-CA-CCGCCGGTTCGTA
seq0014        -------------------------GTGCG-CATGAACTAGGC-CA-CCGCCTGCTCGT-
seq0015        -------------------------GGGCG-CATGAACTAGGC-CACCCGCCTCTTCGTA
seq0018        TTCCCAATGGCACTTGATTGTAAAGGGGCG-CATGAACTAGGC-CA-CCTACGGTTCAAA
seq0020        -------------------------CGGCGCCATGAACTAGGC-CA-CCGGGGGATTATG

(position)     1111111111
               8888888888
               0123456789
                         
seq0000        GTCTGGGAAC
seq0001        GTCTGGGAAC
seq0002        GTCTGGGGAC
seq0003        GTCTGGGGAC
seq0004        GTCTGGGGAC
seq0005        GTCTGGTAAC
seq0006        GTCTGGTAAC
seq0007        GTCTGGTAAC
seq0008        GATTGGTAAC
seq0009        -------AAC
seq0013        GACTGGTCAC
seq0014        GACGGGTAAC
seq0015        GACTCGTT--
seq0018        GACTGGTCAC
seq0020        GACTCGTAAC


<<<<< 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, -2) .

[ 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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0001   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0002   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0006   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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
seq0009   	    -    -    -    -    4    -    -    -    7    7    3    -    -    -    -    -    -    -    -    -    -    -    -    -   16   16 -144 -144    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0
seq0014   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    -    -    3
seq0015   	    -    -    -    -    4    4    4    0    0    0  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    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   	    -    -    -    -    4    4    4    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    0    0    0    0    0    0
seq0020   	    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    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   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    0    0    0   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    3    3    3    3    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0   -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    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0   -1    -    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -24  -24
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0
seq0018   	    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    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189

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seq0005   	    -    1    0    0    0    0    0    0    0    0    0    0    0    -    1    1    -    2    2    1    1    1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2
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seq0008   	    -    1    0    0    0    0    0    0    0    0    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   -2   -2
seq0009   	    -  -23  -23  -23  -23  -23  -23  -25  -25  -25  -25  -25  -25  -25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0013   	    -    1    0    0    0    0    0    0    0    0    0    0    0    -    1    1    -    2    2    1    1    1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2
seq0014   	    -    1    0    0    0    0    0    0    0    0    0    0    0    -    1    1    -    2    2    1    1    1   -1   -1   -1   -1   -1   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2
seq0015   	    -    1    0    0    0    0    0    0    0    0    0    0    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    -    -
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<<<<< 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). >>>>>

SKIPPED the Calculation, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


