<<<<< 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 = 80 ,
#{Sites in the segment}_rec = 77 .


<< Correspondence between sequence IDs and sequence indices >>

Indx:	Seq_ID

0:	seq0000
1:	seq0001
2:	seq0002
3:	seq0003
4:	seq0004
5:	seq0005
6:	seq0006
7:	seq0007
8:	seq0008
9:	seq0009
10:	seq0013
11:	seq0014
12:	seq0015
13:	seq0018
14:	seq0020


<< Original Segment of the Reference Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---------------AGAGTAATACTTAATAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0001        ---------------AGAGTAATACTTAATAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0002        CAATTAAGACGACCA-GAGTAATACTTAATAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0003        CCATTAAGACGACCA-GAGTAATACTTAATAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0004        CAATTAAGACGACCA-GAGTAATACTTAATAG---TCCTCGCTAATTG-G--GGAAGGAG
seq0005        ---------------AGAGGGATACTTAATAG---GCGTCGCTAATTG-GCGGGAAGGAG
seq0006        ---------------AGAGTAATACTTAATAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0007        ---------------AGAGTAATACTTAATAG---TCGTCGCTACTTG-G--GGAACAAG
seq0008        ---------------AGAATAATACTTCATAG---TCGTCACTGATTG-G--GGAAGGAG
seq0009        ---------------AGAGCAATACTCACTAG---TCGTCGCTAATTG-G--GGAAGGAG
seq0013        ---------------ACAGAAATACTTAAGAG---TTGTCGCTAATTGTG--GGAAGGAG
seq0014        ---------------AGCGTAA--------------------------------------
seq0015        ---------------AGAGTAATACTTAATAT---CTCTCGCTAATTG-C--GGTAGGAG
seq0018        ---------------AGAGTCATTCTTAATAGTCTTGGTCGCTAATTG-G--GGAAGGAC
seq0020        ---------------GGCGACATACTTAA-------------------------------

(position)     66666666667777777777
               01234567890123456789
                                   
seq0000        GAGGGCT---TATAAAAGAC
seq0001        GAGGGCT---TATAAAAGAC
seq0002        GAGGGCT---TATAAAAGAC
seq0003        GAGGGCT---TATAAAAGAC
seq0004        GAGGGCT---TATAAAAGAC
seq0005        GCGGGCT---GATAAAAGAC
seq0006        GCGGGCT---GATAAAAGAC
seq0007        GCGGGCT---GATAAAAGAC
seq0008        GA--GCTTTCGATAAAA-AG
seq0009        GA--GCT---GTGAAAAGAC
seq0013        -A--ACT---GATAAAAGC-
seq0014        ------T---GATAAAAGAC
seq0015        GA--GCT---GATAAAAGAC
seq0018        GA--GTT---GCTAAGAGAC
seq0020        -----------------GAC


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --------------AGAGTAATACTTAATAGTC---GTCGCTAATTG--GGGAAGGAGGA
seq0001        --------------AGAGTAATACTTAATAGTC---GTCGCTAATTG--GGGAAGGAGGA
seq0002        CAATTAAGACGACCAGAGTAATACTTAATAGTC---GTCGCTAATTG--GGGAAGGAGGA
seq0003        CCATTAAGACGACCAGAGTAATACTTAATAGTC---GTCGCTAATTG--GGGAAGGAGGA
seq0004        CAATTAAGACGACCAGAGTAATACTTAATAGTC---CTCGCTAATTG--GGGAAGGAGGA
seq0005        --------------AGAGGGATACTTAATAGGC---GTCGCTAATTGGCGGGAAGGAGGC
seq0006        --------------AGAGTAATACTTAATAGTC---GTCGCTAATTG--GGGAAGGAGGC
seq0007        --------------AGAGTAATACTTAATAGTC---GTCGCTACTTG--GGGAACAAGGC
seq0008        --------------AGAATAATACTTCATAGTC---GTCACTGATTG--GGGAAGGAGGA
seq0009        --------------AGAGCAATACTCACTAGTC---GTCGCTAATTG--GGGAAGGAGGA
seq0013        --------------ACAGAAATACTTAAGAGTT---GTCGCTAATTG--TGGGAAGGAGA
seq0014        --------------A-----------------------------------------GCGT
seq0015        --------------AGAGTAATACTTAATATCT---CTCGCTAATTG--CGGTAGGAGGA
seq0018        --------------AGAGTCATTCTTAATAGTCTTGGTCGCTAATTG--GGGAAGGACGA
seq0020        --------------GGCGACATACTTA---------------------------------

(position)     66666666667777777
               01234567890123456
                                
seq0000        GGGCTTA-TA-AAAGAC
seq0001        GGGCTTA-TA-AAAGAC
seq0002        GGGCTTA-TA-AAAGAC
seq0003        GGGCTTA-TA-AAAGAC
seq0004        GGGCTTA-TA-AAAGAC
seq0005        GGGCTGA-TA-AAAGAC
seq0006        GGGCTGA-TA-AAAGAC
seq0007        GGGCTGA-TA-AAAGAC
seq0008        --GCTTTCGATAAAAAG
seq0009        --GCTGT-GA-AAAGAC
seq0013        --ACTGA-TA-AAAG-C
seq0014        --AATGA-TA-AAAGAC
seq0015        --GCTGA-TA-AAAGAC
seq0018        --GTTGC-TA-AGAGAC
seq0020        -------------AGAC


<<<<< 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, -3) .

[ 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0002   	    0    0    0    0    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   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0003   	    0    0    0    0    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   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0004   	    0    0    0    0    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   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    1
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -4   -4    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -    -    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -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

seq0000   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0001   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0002   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0003   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0004   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0005   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0006   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0007   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0008   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3
seq0009   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0013   	    1   -1   -1   -1   -1   -1   -1   -1   -1   -2    -    -   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3    -   -2
seq0014   	    -    -    -    -    -    -   40   40   40   40    -    -   42   42   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0015   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0018   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -   -2   -2   -2   -5   -5    -   -4   -4    -   -3   -3   -3   -3   -3   -3
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   45   -3   -3   -3




[INFORMATION] The original $commoner_shift_flank = -3. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0002   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0003   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0004   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -1    -    -    -    2    2    2    2    2    2    2    2    2    2    2
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    2    2
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    2    2    2    2    2    2    2    2    2    2    2    2    2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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

seq0000   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0001   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0002   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0003   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0004   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0006   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0007   	    -    -    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0008   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0
seq0009   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0013   	    -    -    4    4    2    2    2    2    2    2    2    2    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    -    1
seq0014   	    -    -    -    -    -    -    -    -    -   43   43   43   43    -    -   45   45    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0015   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0018   	    -    -    3    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1   -2   -2    -   -1   -1    -    0    0    0    0    0    0
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48    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} = 18) >>

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

0	3	17	8	18	3	n/a	2,3,4
1	17	33	25	12	2	n/a	0,1,5,6,7,8,9,10,12
2	17	17	21	14	2	n/a	11
3	17	49	26	13	2	n/a	13
4	17	29	28	10	2	n/a	14
5	18	33	8	16	2	n/a	2,3,4
6	34	49	25	2,11	-1,2	0	0,1,2,3,4,5,6,7,8,9,10,12
7	50	67	10	9	1	n/a	5
8	52	52	27	17	3	n/a	0,1,2,3,4,6,7,8,9,12,13
9	52	67	20	19,15,7	4,2,1	0,0	10
10	53	67	27	4	1	n/a	0,1,2,3,4,6,7,9,12,13
11	53	77	16	6	1	n/a	8
12	59	66	21	20,21	43,45	0	11
13	67	67	21	5	1	n/a	11
14	68	69	27	0	-2	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13
15	71	72	27	1	-1	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13
16	76	76	28	22	48	n/a	14
17	79	79	20	8	1	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} = 18) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 2): 14, 15 . ]


[ 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	15	15	Merge(complementary)	8:15:15:X/8:0:14:-	8:3:16:-
1	0	17	17	NO_ASSOCIATED_EVENT(???)	26:32:34:-	None
2	0	1	1	Complex(???)	None	21:18:58:X
3	0	33	33	Shift(???)	26:32:34:-	26:36:38:-
4	0	13	13	Complex(???)	None	27:30:75:-
5	0	16	16	Complex(???)	8:15:15:X	None
6	0	13	16	NO_ASSOCIATED_EVENT(???)	26:32:34:-	None
7	0	18	18	Shift(???)	10:50:51:-	10:50:51:-
8	0	1	1	NO_ASSOCIATED_EVENT(???)	20:48:48:-	None
9	0	19	16	Complex(???)	20:48:48:-	None
10	0	15	15	Complex(???)	22:60:60:X	None
11	0	25	25	Complex(???)	16:77:77:X/16:67:69:-	16:70:70:-/16:73:73:-
12	0	6	8	Complex(???)	21:22:65:X	21:18:58:X
13	0	1	1	Complex(???)	21:22:65:X	None
14	Skipped!!(NO_RELEVANT_BRANCH)
15	Skipped!!(NO_RELEVANT_BRANCH)
16	0	1	1	Shift	27:29:76:-	27:30:75:-
17	0	1	1	Shift	20:79:79:X	20:78:78:X


[ Contents of %indel_ref2assoc_cblks ]

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

8:0:14	0
8:15:15	0,5
21:22:65	12,13
27:29:76	16
26:32:34	1,3,6
20:48:48	8,9
10:50:51	7
22:60:60	10
15:62:63	{Equivalent to '15:63:64'(rec)}
16:67:69	11
16:77:77	11
20:79:79	17


[ Contents of %indel_rec2assoc_cblks ]

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

8:3:16	0
21:18:58	2,12
27:30:75	4,16
26:36:38	3
10:50:51	7
15:63:64	{Equivalent to '15:62:63'(ref)}
16:70:70	11
16:73:73	11
20:78:78	17


<<<< (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]

1	=> [3],


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

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

3	=> [1],


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

Indx_cblk_A	indx_cblk_B

0	5
16	4


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

[ For the 1 th pair: (0, 5) ]


{ The representative path is: 0  -> 5 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	1	15	1	1	8	2,3,4	2,3,4
2nd(reconstructed)	3	33	2	2	8	2,3,4	2,3,4


( Errors associated with the c-blocks )

Subject_c-block	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	8:15:15:X/8:0:14:-	8:1:16:-
2nd(reconstructed)	Merge(complementary)	8:32:33:X/8:1:16:-	8:3:16:-


[ For the 2 th pair: (16, 4) ]


{ The representative path is: 4  -> 16 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	17	30	2	2	28	14	14
2nd(reconstructed)	76	76	46	46	28	14	14


( Errors associated with the c-blocks )

Subject_c-block	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift(???)	27:29:76:-	27:31:76:-
2nd(reconstructed)	Shift	27:31:76:-	27:30:75:-


