<<<<< 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 = 74 ,
#{Sites in the segment}_rec = 60 .


<< 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        TT---G--ATGA------------------------------------------------
seq0001        TT---G--ATG-------------------------------------------------
seq0002        TT---G--ATGA------------------------------------------------
seq0003        TT---G--ATGA------------------------------------------------
seq0004        TT---G--ATGA------------------------------------------------
seq0005        TT---G--ATGA------------------------------------------------
seq0006        TT---G--ATGG------------------------------------------------
seq0007        TT---G--ATGA------------------------------------------------
seq0008        TT---G--AGGG------------------------------------------------
seq0009        TA---G--AGGA------------------------------------------------
seq0013        AA---GTAAGGA------------------------------------------------
seq0014        ACTCCG--AGGA------------------------------------------------
seq0015        AA---G--AGGA------------------------------------------------
seq0018        TA---C--AGAA------------------------------------------------
seq0020        AA---G--GGTAAATCCTCGGGACATGTAGAGTGAACAGCTTAGGTATCCTTCAAATCCA

(position)     66666666667777
               01234567890123
                             
seq0000        --CTC---ATGATA
seq0001        -------------A
seq0002        --CTC---ATGTTA
seq0003        --CTC---ATGTTA
seq0004        --CTC---ATGTTA
seq0005        --CTC---CTGAT-
seq0006        --CTC---ATGAT-
seq0007        --CTC---ATGAT-
seq0008        --CTC---ATGATA
seq0009        --CAC---ATGATA
seq0013        --CTC---AAGATA
seq0014        --TTC---GTGATT
seq0015        --CTCCTGATGATA
seq0018        --CTC---GTGCTA
seq0020        TA------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---TTGATGA----CTCATG-------------------------------------ATA
seq0001        ---TTGATGA--------------------------------------------------
seq0002        ---TTGATGA----CTCATG-------------------------------------TTA
seq0003        ---TTGATGA----CTCATG-------------------------------------TTA
seq0004        ---TTGATGA----CTCATG-------------------------------------TTA
seq0005        ---TTGATGA----CTCCTG-------------------------------------AT-
seq0006        ---TTGATGG----CTCATG-------------------------------------AT-
seq0007        ---TTGATGA----CTCATG-------------------------------------AT-
seq0008        ---TTGAGGG----CTCATG-------------------------------------ATA
seq0009        ---TAGAGGA----CACATG-------------------------------------ATA
seq0013        AAGTA-AGGA----CTCAAG-------------------------------------ATA
seq0014        ACTCCGAGGA----TTCGTG-------------------------------------ATT
seq0015        AAGAGGACTC----CTGATG-------------------------------------ATA
seq0018        ---TACAGAA----CTCGTG-------------------------------------CTA
seq0020        ---AAGGGTAAATCCTCGGGACATGTAGAGTGAACAGCTTAGGTATCCTTCAAATCCATA


<<<<< 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, -14) .

[ 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   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    3    3    0   -2   -2   -2  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0   -3   -3   -3    -   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    0    0    0    0    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    0   -3   -5   -5   -5   -5  -55  -55  -55    -    -    -    -  -51  -51  -51  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    3    0   -2   -2   -2   -2    -    -    -    -  -48  -48  -48  -51  -51  -51    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    3    3    0   -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   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2



(position)	   50   51   52   53   54   55   56   57   58   59

seq0000   	    -    -    -    -    -    -    -  -14  -14  -14
seq0001   	    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -  -14  -14  -14
seq0003   	    -    -    -    -    -    -    -  -14  -14  -14
seq0004   	    -    -    -    -    -    -    -  -14  -14  -14
seq0005   	    -    -    -    -    -    -    -  -14  -14    -
seq0006   	    -    -    -    -    -    -    -  -14  -14    -
seq0007   	    -    -    -    -    -    -    -  -14  -14    -
seq0008   	    -    -    -    -    -    -    -  -14  -14  -14
seq0009   	    -    -    -    -    -    -    -  -14  -14  -14
seq0013   	    -    -    -    -    -    -    -  -14  -14  -14
seq0014   	    -    -    -    -    -    -    -  -14  -14  -14
seq0015   	    -    -    -    -    -    -    -  -14  -14  -14
seq0018   	    -    -    -    -    -    -    -  -14  -14  -14
seq0020   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2




[INFORMATION] The original $commoner_shift_flank = -14. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12  -50    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   14   14   11   11   11    -   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   14   14   14   14   14   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   14   14   11    9    9    9    9  -41  -41  -41    -    -    -    -  -37  -37  -37  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12    -    -    -    -  -34  -34  -34  -37  -37  -37    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   17   17   14   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12



(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

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0
seq0020   	   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12



<<<<< 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	14	15	24	12	14	n/a	10,12
1	14	19	21	13	14	n/a	11
2	16	18	20	7	11	n/a	10
3	16	33	23	6,5,1,3	11,9,-41,-37	0,0,0	12
4	17	19	29	14,11	17,14	0	0,1,2,3,4,5,6,7,8,9,13,14
5	20	23	27	8	12	n/a	0,2,3,4,5,6,7,8,9,10,11,13
6	20	22	2	10	12	n/a	1
7	20	73	28	9	12	n/a	14
8	23	23	2	0	-50	n/a	1
9	28	30	27	4	-34	n/a	0,2,3,4,5,6,7,8,9,10,11,13
10	31	33	27	2	-37	n/a	0,2,3,4,5,6,7,8,9,10,11,13



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


[ Skipped Composite-Blocks (#{cblocks} = 4): 0, 5, 9, 10 . ]


[ 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	Skipped!!(NO_RELEVANT_BRANCH)
1	0	6	6	Complex(???)	21:2:4:-/20:6:7:-	20:19:19:X
2	0	3	3	Complex(???)	20:6:7:-/21:2:4:-	20:19:19:X
3	0	66	18	Complex(???)	23:65:67:-	None
4	0	6	3	Complex(???)	None	24:14:16:-
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	3	3	Complex(???)	2:11:72:X	None
7	0	54	54	Complex(???)	27:62:73:-/28:12:61:-	28:24:27:-/28:34:70:-
8	0	1	1	Shift	2:11:72:X	2:28:73:X
9	Skipped!!(NO_RELEVANT_BRANCH)
10	Skipped!!(NO_RELEVANT_BRANCH)


[ Contents of %indel_ref2assoc_cblks ]

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

21:2:4	1,2
20:6:7	1,2
2:11:72	6,8
28:12:61	7
27:62:73	7
23:65:67	3
14:73:73	None


[ Contents of %indel_rec2assoc_cblks ]

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

24:14:16	4
20:19:19	1,2
28:24:27	7
2:28:73	8
28:34:70	7
14:73:73	None


<<<< (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} = 3) ]

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

0	=> [1],
5	=> [7],
10	=> [3],


[ Contents of %cb2hard_linking (#{keys} = 3) ]

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

1	=> [0],
3	=> [10],
7	=> [5],


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

Indx_cblk_A	indx_cblk_B

1	2
8	6


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

[ For the 1 th pair: (1, 2) ]


{ The representative path is: 1  -> 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)	3	8	3	3	21	10,11,12	11
2nd(reconstructed)	14	19	11	11	20	10,11,12	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)	Partial-Neighborng-Branch-Merge(+slide(?))(?)	21:2:4:-/20:6:7:-	21:8:8:-/22:5:7:-
2nd(reconstructed)	Complex(???)	21:8:8:-	20:19:19:X


[ For the 2 th pair: (8, 6) ]

