<<<<< 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 = 121 ,
#{Sites in the segment}_rec = 121 .


<< 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        TATACAGCTCCTGTAA-AAAAACAAGCCT-------------------------------
seq0001        TATACAGCTCCTTTAA-AAAAACAAGCCT-------------------------------
seq0002        TATACAGCTCCTTGAA-AAAAACAAGCCT-------------------------------
seq0003        TATACAGCTCCTTGAA-AAAAACAAGCCT-------------------------------
seq0004        TATACAGCTCCTTGAA-AAAAACAAGCCT-------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        TATCCCTCTCCTTGGG-AAAAACAAGGCT-------------------------------
seq0009        TATCGACCTCCTTGGG-AAAAACAAGGCC-------------------------------
seq0013        CATACCGGTTCTTGAG-AGAAACAAGGAT-------------------------------
seq0014        TATACCTCTCCTCGTGTCATAACACGGGTAGCCTGATATGTACGACTTTCGTCTGAAATA
seq0015        TATACCTGTCGTTGAG-GTA-ACAAGTCT-------------------------------
seq0018        TATACCTCTCCTTGAG-ATAACC-AGGAT-------------------------------
seq0020        TATACCTCACCTCGGG-AAAGCCAAGGCT-------------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -----------------------------AGGATTCTCGGGTTCTCCCTTTCATTCGAAG
seq0001        -----------------------------AGGATTCTCGGGTTCTCCCTTTCATTCGAAG
seq0002        -----------------------------AGGATTCTAGGGTTCTCCCTTTCATTCGAAG
seq0003        -----------------------------AGGATTCTAGGGTTCTCCCTTTCATTCGAAG
seq0004        -----------------------------AGGATTCTATGGTTCTCCCTTTCATTCGAAA
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        -----------------------------AGGATTCCCGGGCTCTCCCTTTCATTCGGCG
seq0009        -----------------------------AGGGTCCTCGGCGCCTCCATTTCACTCGGAG
seq0013        -----------------------------TGGATTATCGTTTTCTCCTTCTC-TTCGAGG
seq0014        CACATCTGTCATATTGGTAAGGCCCATGAGGGGTTCTCGGTTTCTTCTGATCATTCGGGG
seq0015        -----------------------------CGGATTCCCGGTTTCTCCTTATCATTCGAGT
seq0018        -----------------------------GGGATTCTCGGTTTCTCCCTTACTGTCGTTG
seq0020        -----------------------------GGGATTCTCGGTCTCTGCCTTTCATTCGGCG

(position)     1
               2
               0
                
seq0000        G
seq0001        G
seq0002        G
seq0003        G
seq0004        G
seq0005        -
seq0006        -
seq0007        -
seq0008        C
seq0009        A
seq0013        G
seq0014        G
seq0015        G
seq0018        G
seq0020        G


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TATACAGCTCCTGTAAAAA-AACAAGC---------------------------------
seq0001        TATACAGCTCCTTTAAAAA-AACAAGC---------------------------------
seq0002        TATACAGCTCCTTGAAAAA-AACAAGC---------------------------------
seq0003        TATACAGCTCCTTGAAAAA-AACAAGC---------------------------------
seq0004        TATACAGCTCCTTGAAAAA-AACAAGC---------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        TATCCCTCTCCTTGGGAAA-AACAAGG---------------------------------
seq0009        TATCGACCTCCTTGGGAAA-AACAAGG---------------------------------
seq0013        CATACCGGTTCTTGAGAGA-AACAAGG---------------------------------
seq0014        TATACCTCTCCTCGTGTCATAACACGGGTAGCCTGATATGTACGACTTTCGTCTGAAATA
seq0015        TATACCTGTCGTTGAG-GT-AACAAGT---------------------------------
seq0018        TATACCTCTCCTTGAGAT--AACCAGG---------------------------------
seq0020        TATACCTCACCTCGGGAAA-GCCAAGG---------------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------CTAGG---------------ATTCTCGGGTTCTCCCTTTCATTCGAAG
seq0001        ------------CTAGG---------------ATTCTCGGGTTCTCCCTTTCATTCGAAG
seq0002        ------------CTAGG---------------ATTCTAGGGTTCTCCCTTTCATTCGAAG
seq0003        ------------CTAGG---------------ATTCTAGGGTTCTCCCTTTCATTCGAAG
seq0004        ------------CTAGG---------------ATTCTATGGTTCTCCCTTTCATTCGAAA
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------CTAGG---------------ATTCCCGGGCTCTCCCTTTCATTCGGCG
seq0009        ------------CCAGG---------------GTCCTCGGCGCCTCCATTTCACTCGGAG
seq0013        ------------ATTGG---------------ATTATCGTTTTCTCCTTCTC-TTCGAGG
seq0014        CACATCTGTCATATTGGTAAGGCCCATGAGGGGTTCTCGGTTTCTTCTGATCATTCGGGG
seq0015        ------------CTCGG---------------ATTCCCGGTTTCTCCTTATCATTCGAGT
seq0018        ------------ATGGG---------------ATTCTCGGTTTCTCCCTTACTGTCGTTG
seq0020        ------------CTGGG---------------ATTCTCGGTCTCTGCCTTTCATTCGGCG

(position)     1
               2
               0
                
seq0000        G
seq0001        G
seq0002        G
seq0003        G
seq0004        G
seq0005        -
seq0006        -
seq0007        -
seq0008        C
seq0009        A
seq0013        G
seq0014        G
seq0015        G
seq0018        G
seq0020        G


<<<<< 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, 0) .

[ 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   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    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    0    0    0    0    0    0    -    0    0    -    1    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    1    1    1    1    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1    -    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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   45  -15  -15  -15    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120

seq0000   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0    0    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
seq0003   	    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
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    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    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    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    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



<<<<< 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 ...


