<<<<< 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 = 104 ,
#{Sites in the segment}_rec = 103 .


<< 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        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0001        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0002        CCCGGTCGCCGATCG---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0003        TCCGGTC--CGATCT---GTGTTGCTTCCCTTGTGGGGTATCAGA-CGCTGG--------
seq0004        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0005        GCCGGTCGCCGATAT---GTGTTGCTTCTCTTGTGGGGGACCCGA-CGCTGG--------
seq0006        GCCGGTTGCCGATCT---GTGTTGCTTCCCTTGTGGGGGATCCGA-CGCTGG--------
seq0007        GCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGGATCCGA-CGCTGG--------
seq0008        ------------------------------------------------------------
seq0009        TCCGGTCACCGATCT---GTGTGGCTTCCCTGTTGGTGGAGCCGA-CACTAGTATTAGAC
seq0013        TCCGGCGTCCGATTT---GTGTTGCTTCCCTTGTGGGGGCGCCAA-CGCTGGTCTTCAAT
seq0014        TCCGGTGTACGATCT---ATGTCGCTTTCCGTGTGGGGGGGTAAA-CGCTGGCCTTCGAT
seq0015        TCCGTAGTGCGATCT---GAGTTGCTTCCCTTGTGGGGGGGTAAA-CGCTGGTCTTCGAG
seq0018        GCGGGTGACCGATCT---GTTCTGCTTCCCTTGTGGGGGAGCCGATTGCTGGTAGTCGGT
seq0020        TCAGGTGGCCGATCTGGAGTATTGCTTCCGTTTGGGGGGGGCCGA-CGCTGGTATTCGAT

(position)     00000000000000000000000000000000000000001111
               66666666667777777777888888888899999999990000
               01234567890123456789012345678901234567890123
                                                           
seq0000        --------------------------------------------
seq0001        --------------------------------------------
seq0002        --------------------------------------------
seq0003        --------------------------------------------
seq0004        --------------------------------------------
seq0005        --------------------------------------------
seq0006        --------------------------------------------
seq0007        --------------------------------------------
seq0008        --------ATGAGTT-AGAACATAATCC--TG-T-AAC----CA
seq0009        TAAGGGGTATGAGTT-AGAACATATTCG--TG-TGAAC----AA
seq0013        TAT---GGA-GAG-TAAGATCCTATTAC--CG-T-AACCATGAA
seq0014        TAT---GGATGAGGTAAGAGCCCATTAT--TC-A-AACGAAGAA
seq0015        TAT---GGATGAGTTAAGATTCTATTAC--TG-C-AATCCACGA
seq0018        TACGATTGACGAGCTTTGATCGTATTAC--TG-T-TACTAAGAA
seq0020        TATGAAGGAAGAGTTATCATCATATTACATAGAT-AAGCAAGAA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0001        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0002        CCCGGTCGCCGATCG---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0003        TCCGGT--CCGATCT---GTGTTGCTTCCCTTGTGGGGTATCAGA-CGCTGG--------
seq0004        TCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGTGTCAGA-CGCTGG--------
seq0005        GCCGGTCGCCGATAT---GTGTTGCTTCTCTTGTGGGGGACCCGA-CGCTGG--------
seq0006        GCCGGTTGCCGATCT---GTGTTGCTTCCCTTGTGGGGGATCCGA-CGCTGG--------
seq0007        GCCGGTCGCCGATCT---GTGTTGCTTCCCTTGTGGGGGATCCGA-CGCTGG--------
seq0008        A-----------------------------------------------------------
seq0009        TCCGGTCACCGATCT---GTGTGGCTTCCCTGTTGGTGGAGCCGA-CACTAGTATTAGAC
seq0013        TCCGGCGTCCGATTT---GTGTTGCTTCCCTTGTGGGGGCGCCAA-CGCTGGTCTTCAAT
seq0014        TCCGGTGTACGATCT---ATGTCGCTTTCCGTGTGGGGGGGTAAA-CGCTGGCCTTCGAT
seq0015        TCCGTAGTGCGATCT---GAGTTGCTTCCCTTGTGGGGGGGTAAA-CGCTGGTCTTCGAG
seq0018        GCGGGTGACCGATCT---GTTCTGCTTCCCTTGTGGGGGAGCCGATTGCTGGTAGTCGGT
seq0020        TCAGGTGGCCGATCTGGAGTATTGCTTCCGTTTGGGGGGGGCCGA-CGCTGGTATTCGAT

(position)     0000000000000000000000000000000000000000111
               6666666666777777777788888888889999999999000
               0123456789012345678901234567890123456789012
                                                          
seq0000        -------------------------------------------
seq0001        -------------------------------------------
seq0002        -------------------------------------------
seq0003        -------------------------------------------
seq0004        -------------------------------------------
seq0005        -------------------------------------------
seq0006        -------------------------------------------
seq0007        -------------------------------------------
seq0008        ----------TGAGTTAGAACATAATCC---TGT----AACCA
seq0009        TAAGGGGTA-TGAGTTAGAACATATTCG---TGT---GAACAA
seq0013        TATGGA-----GAGTAAGATCCTATTAC---CGTAACCATGAA
seq0014        TATGGAT---GAGGTAAGAGCCCATTAT---TCAAACGAAGAA
seq0015        TATGGAT---GAGTTAAGATTCTATTAC---TGCAATCCACGA
seq0018        TACGATTGACGAGCTTTGATCGTATTAC---TGTTACTAAGAA
seq0020        TATGAAGGAAGAGTTATCATCATATTACATAGATAAGCAAGAA


<<<<< 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   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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    -    -    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    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    0    0    0    0    0    -    0    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    -    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    -    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    -    0    0    0    0
seq0008   	  -68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    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    0    0    0    0    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   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    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    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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    -    3    3
seq0009   	    0    0    0    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    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0    -    -    -    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3    -    -    -    -    -    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
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    -    -    -    1    1    0   -1   -1   -1   -1   -1   -1
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   -1   -1   -1   -1   -1   -1



(position)	  100  101  102

seq0000   	    -    -    -
seq0001   	    -    -    -
seq0002   	    -    -    -
seq0003   	    -    -    -
seq0004   	    -    -    -
seq0005   	    -    -    -
seq0006   	    -    -    -
seq0007   	    -    -    -
seq0008   	    3   -1   -1
seq0009   	    3   -1   -1
seq0013   	   -1   -1   -1
seq0014   	   -1   -1   -1
seq0015   	   -1   -1   -1
seq0018   	   -1   -1   -1
seq0020   	   -1   -1   -1



<<<<< 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} = 11) >>

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

0	0	0	16	0	-68	n/a	8
1	8	8	5	12	2	n/a	3
2	63	65	20	2	-3	n/a	10
3	63	66	24	1	-3	n/a	11,12
4	70	75	18	10	1	n/a	8,9
5	71	73	20	11	1	n/a	10
6	91	92	27	9	1	n/a	8,9,10,11,12,13
7	94	102	29	3	-1	n/a	10,11,12,13,14
8	97	100	17	14	3	n/a	9
9	98	100	16	13	3	n/a	8
10	101	102	18	4	-1	n/a	8,9



<<<<< 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} = 11) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 1): 6 . ]


[ 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	1	1	Shift	16:0:67:X	16:1:68:X
1	0	1	1	Shift	5:7:8:X	5:6:7:X
2	0	3	3	Complex(???)	20:69:69:X	20:66:70:X
3	0	4	4	Complex(???)	24:63:65:X	24:67:68:X
4	0	6	6	Complex(???)	19:75:75:X	16:1:68:X
5	0	3	3	Merge(same-type)	20:69:69:X/20:73:73:X	20:66:70:X
6	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
7	0	9	9	Complex(???)	19:98:101:X/15:52:103:X	19:94:96:X/15:52:102:X
8	0	4	4	Complex(???)	17:94:94:-	16:97:97:X
9	0	3	3	Complex(???)	17:94:94:-	16:97:97:X
10	0	2	2	Complex	19:98:101:X/15:52:103:X	15:52:102:X


[ Contents of %indel_ref2assoc_cblks ]

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

16:0:67	0
5:7:8	1
28:15:17	{Equivalent to '28:15:17'(rec)}
26:45:45	{Equivalent to '26:45:45'(rec)}
15:52:103	7,10
24:63:65	3
20:69:69	2,5
20:73:73	5
19:75:75	4
28:88:89	None
28:92:92	None
17:94:94	8,9
19:98:101	7,10


[ Contents of %indel_rec2assoc_cblks ]

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

16:1:68	0,4
5:6:7	1
28:15:17	{Equivalent to '28:15:17'(ref)}
26:45:45	{Equivalent to '26:45:45'(ref)}
15:52:102	7,10
20:66:70	2,5
24:67:68	3
25:69:69	None
28:88:90	None
19:94:96	7
16:97:97	8,9


<<<< (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} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linked,by,the,key]

9	=> [8],
10	=> [7],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

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

7	=> [10],
8	=> [9],


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

Indx_cblk_A	indx_cblk_B

0	4
5	2


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

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

[ For the 2 th pair: (5, 2) ]


{ The representative path is: 5  -> 2 }


( 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)	71	73	1	1	20	10	10
2nd(reconstructed)	63	65	-3	-3	20	10	10


( 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(???)	20:69:69:X/20:73:73:X	20:70:70:X
2nd(reconstructed)	Complex	20:63:65:X/20:70:70:X/21:67:68:X	20:66:70:X


