<<<<< 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 = 133 ,
#{Sites in the segment}_rec = 131 .


<< 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        CTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGGTGCC-CAGTAATAGGGTAGAGC
seq0001        CTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGCTGCC-CAGTAATAGGGTAGAGC
seq0002        CTT---------------------------------------------------------
seq0003        CTT---------------------------------------------------------
seq0004        CTT---------------------------------------------------------
seq0005        CTACAGCACTGGGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGATC
seq0006        CTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGATC
seq0007        GTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGATC
seq0008        T-----------------------TCCTAGTGCCATGA-GCTCCAGTAAAAAGGTAGAGC
seq0009        C----------------------CTCCTAGTGCCATGATGCCCGAATAATAAGGTAGTGC
seq0013        CTTCTGCACC---ATCGCACTTC--TCTAGAGCGGCGACGCCCCAGTA--AAGAGAGAGC
seq0014        CATCTGCTCT---ACCGAACTACCTCCTAGAGCCATGATGCCCCGTTA--ACGAGCGAAA
seq0015        GCTCTGCACT---GTCGAACTATCT--TAGGGCCATGATCCTCCGGTA--AAGTTAGAGC
seq0018        CTTCAGCACT---TTCGATCCACTGCCTGGAGCCA---------AGTG--AATAGAGAGC
seq0020        CTCCAGCACA---ATTGAACTACTTCCTAGGGCCTTAATGCCCG-G-A--AAGACGGAGC

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GTTCGCACCCAG--TGC--------A-----------CCACG------------------
seq0001        GTTCGCACCCAG--TGC--------A-----------CCACG------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        TTTCGCGCCCAG--TGC--------A-----------ACACG------------------
seq0006        TTTCGCGCCCAG--TGC--------A-----------AAACG------------------
seq0007        TTTCGCGCCCAG--TGC--------A-----------ACACG------------------
seq0008        TTTAGCAGCCTG--AGC--------A-----------AAACC------------------
seq0009        TTTCTCACCCTG--AGC--------A-----------GCGCC------------------
seq0013        CTTCACACCCAG--AGC--------ATACGATACGCCT----------------------
seq0014        TTTCGCGCCCAG--TGG--------CTTAGATAGGTCTCACA------------------
seq0015        TTTCGCACCAAGGTTGC--GGGCATATACGATAGACCTCACA------------------
seq0018        TTGCGCTCCCAG--TGC--------ATAAGATAGGGGTCACACGGTTAATAATATGGCGT
seq0020        TTGCGCACCTAG--TGCTA------ATAAGATTGGCGTCACA------------------

(position)     1111111111111
               2222222222333
               0123456789012
                            
seq0000        ------CTGCAAA
seq0001        ------CTGCAAA
seq0002        -------------
seq0003        -------------
seq0004        -------------
seq0005        ------CTGTAAA
seq0006        ------CTGTAAA
seq0007        ------CTGTAAA
seq0008        ------CTGCAAA
seq0009        ------CTGC--A
seq0013        --------GCA--
seq0014        ------CTGCG--
seq0015        ------CTCCA--
seq0018        GTACGGCTGGAAA
seq0020        ------CCGCAAA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGGTGCCC-AGTAATAGGGTAGAGC
seq0001        CTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGCTGCCC-AGTAATAGGGTAGAGC
seq0002        CTT---------------------------------------------------------
seq0003        CTT---------------------------------------------------------
seq0004        CTT---------------------------------------------------------
seq0005        CTACAGCACTGGGAACGAACTTCCTCATAGAGCCATGATGCCC-AGTAATAAGGTAGATC
seq0006        CTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCCC-AGTAATAAGGTAGATC
seq0007        GTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCCC-AGTAATAAGGTAGATC
seq0008        -----------------------TTCCTAGTGCCATGAGCTCC-AGTAAAAAGGTAGAGC
seq0009        ----------------------CCTCCTAGTGCCATGATGCCCGAATAATAAGGTAGTGC
seq0013        CTTCTGCACCAT---CGCACTTC--TCTAGAGCGGCGACGCCCCAGTA--AAGAGAGAGC
seq0014        CATCTGCTCTAC---CGAACTACCTCCTAGAGCCATGATGCCCCGTTA--ACGAGCGAAA
seq0015        GCTCTGCACTGT---CGAACTA--TCTTAGGGCCATGATCCTCCGGTA--AAGTTAGAGC
seq0018        CTTCAGCACTTT---CGATCCACTGCCTGGAGCCA---------AGTG--AATAGAGAGC
seq0020        CTCCAGCACAAT---TGAACTACTTCCTAGGGCCTTAATGCCC--GGA--AAGACGGAGC

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GTTCGCACCCAG------TGCACC-------------ACGCTGCAA--------------
seq0001        GTTCGCACCCAG------TGCACC-------------ACGCTGCAA--------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        TTTCGCGCCCAG------TGCAAC-------------ACGCTGTAA--------------
seq0006        TTTCGCGCCCAG------TGCAAA-------------ACGCTGTAA--------------
seq0007        TTTCGCGCCCAG------TGCAAC-------------ACGCTGTAA--------------
seq0008        TTTAGCAGCCTG------AGCAAA-------------ACCCTGCAA--------------
seq0009        TTTCTCACCCTG------AGCAGC-------------GCCCTGC----------------
seq0013        CTTCACACCCAG------AGCATA--CGATACGC------CTGC----------------
seq0014        TTTCGCGCCCAG------TGGCTT--AGATAGGTCTCACACTGC----------------
seq0015        TTTCGCACCAAGGTTGCGGGCATATACGATAGACCTCACACTCC----------------
seq0018        TTGCGCTCCCAG------TGCATA--AGATAGGGGTCACACGGTTAATAATATGGCGTGT
seq0020        TTGCGCACCTAG------TGCTAATAAGATTGGCGTCACACCGCAA--------------

(position)     11111111111
               22222222223
               01234567890
                          
seq0000        ----------A
seq0001        ----------A
seq0002        -----------
seq0003        -----------
seq0004        -----------
seq0005        ----------A
seq0006        ----------A
seq0007        ----------A
seq0008        ----------A
seq0009        ----------A
seq0013        ----------A
seq0014        ----------G
seq0015        ----------A
seq0018        ACGGCTGGAAA
seq0020        ----------A


<<<<< 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   	    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   -1    -    0    0    0    0    0    0
seq0001   	    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   -1    -    0    0    0    0    0    0
seq0002   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    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   -1    -    0    0    0    0    0    0
seq0006   	    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   -1    -    0    0    0    0    0    0
seq0007   	    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   -1    -    0    0    0    0    0    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1    -    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   22    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
seq0013   	    0    0    0    0    0    0    0    0    0    0   -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    0    0    0    0    0    0    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0   -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    0    0    0    0    0    0    0    0    -    -
seq0015   	    0    0    0    0    0    0    0    0    0    0   -3   -3    -    -    -    0    0    0    0    0    0    0    -    -    2    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0   -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    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0   -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    0    0    0    -    -    2    1    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    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0007   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0015   	    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   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4   -4   -4   -4    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    4    4    4    4    4   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2



(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

seq0000   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0001   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0006   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0007   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0008   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0009   	  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2
seq0013   	    4    4  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0014   	  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0015   	  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0
seq0018   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0020   	  -26  -26  -26  -26  -26  -26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2



<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<< Output of 'br_list_classes_shift_respos' >>

$commoner_shift_flank = 0 .


<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

... The MINI-classes increased by 1 compared to the old set!! ...


<<<<< Preliminary (4): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

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


