<<<<< 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 = 18 ,
#{Sites in the segment}_rec = 15 .


<< 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)     000000000011111111
               012345678901234567
                                 
seq0000        AA---GAATC--ACTCGG
seq0001        AA---GAATC--ACTCGG
seq0002        AA---GAATT--ACTCGG
seq0003        AA---GAATT--ACTCTG
seq0004        -------ATT--ACTCGG
seq0005        AA---GAATT--ACTCGG
seq0006        AA---GAATT--ACTCGG
seq0007        AA---GAATT--ACTCGG
seq0008        TA---GACTT--ACTC--
seq0009        AA---AAATT---CTTGG
seq0013        AA---CAATTGCACGCTG
seq0014        AA---CAATT--ACTCGG
seq0015        AA---CAATC--ACTCGG
seq0018        AAACGGCAAG--------
seq0020        AA---GAATG---CTC-C


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111
               012345678901234
                              
seq0000        AAGAATCACTC--GG
seq0001        AAGAATCACTC--GG
seq0002        AAGAATTACTC--GG
seq0003        AAGAATTACTC--TG
seq0004        ----ATTACTC--GG
seq0005        AAGAATTACTC--GG
seq0006        AAGAATTACTC--GG
seq0007        AAGAATTACTC--GG
seq0008        TAGACTTACT----C
seq0009        AAAAATTCTT---GG
seq0013        AACAATTGCACGCTG
seq0014        AACAATTACTC--GG
seq0015        AACAATCACTC--GG
seq0018        AAACGGCA-----AG
seq0020        AAGAATGCTC----C


<<<<< 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

seq0000   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0001   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0002   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0003   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0004   	    -    -    -    -   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0005   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0006   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0007   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0008   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5    -    -    -    -   -1
seq0009   	    0    0   -3   -3   -3   -3   -3   -6   -6   -6    -    -    -   -3   -3
seq0013   	    0    0   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3
seq0014   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0015   	    0    0   -3   -3   -3   -3   -3   -5   -5   -5   -5    -    -   -3   -3
seq0018   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    5
seq0020   	    0    0   -3   -3   -3   -3   -3   -6   -6   -6    -    -    -    -   -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

seq0000   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0001   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0002   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0003   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0004   	    -    -    -    -    -    -    -    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0005   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0006   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0007   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0008   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2    -    -    -    -    2
seq0009   	    -    -    -    3    3    0    0    0    0    0   -3   -3   -3    -    -    -    0    0
seq0013   	    -    -    -    3    3    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0015   	    -    -    -    3    3    0    0    0    0    0   -2   -2   -2   -2    -    -    0    0
seq0018   	    -    -    -    3    3    3    3    3    3    3    3    -    -    -    -    -    8    8
seq0020   	    -    -    -    3    3    0    0    0    0    0   -3   -3   -3    -    -    -    -    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... >>>>>

... 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). >>>>>

<<<<< 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} = 8) >>

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

0	3	4	29	6	3	n/a	0,1,2,3,5,6,7,8,9,10,11,12,14
1	3	10	26	7	3	n/a	13
2	10	13	25	2	-2	n/a	0,1,2,3,4,5,6,7,11,12
3	10	12	28	0	-3	n/a	14
4	10	12	16	3	-2	n/a	8
5	10	12	17	1	-3	n/a	9
6	16	17	26	8	8	n/a	13
7	17	17	16	5	2	n/a	8



<<<<< 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} = 8) >>>>>


[[ 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	1	0	0	0	0
2
3	0	0	3	2	0	0
4	0	0	1	1	0	0
5	1	0	1	1	0	0
6	0	0	1	2	0	0
7	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 2): 0, 2 . ]


[ 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	8	8	Complex(???)	26:2:4:-	26:11:12:X
2	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=3))
3	0	3	3	Complex	25:12:12:-/25:16:16:-/26:13:17:X	25:13:13:-/26:11:12:X
4	0	3	3	Complex(???)	17:12:12:X	18:13:13:X
5	0	3	3	Complex(???)	17:12:12:X/16:16:17:X	18:13:13:X
6	0	2	2	Complex	25:12:12:-	25:13:13:-/27:16:16:-
7	0	1	1	Complex(???)	16:16:17:X	16:16:16:X


[ Contents of %indel_ref2assoc_cblks ]

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

6:0:6	{Equivalent to '6:3:6'(rec)}
26:2:4	1
20:10:11	None
25:12:12	3,6
17:12:12	4,5
26:13:17	3
25:16:16	3
16:16:17	5,7


[ Contents of %indel_rec2assoc_cblks ]

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

6:3:6	{Equivalent to '6:0:6'(ref)}
26:11:12	1,3
25:13:13	3,6
18:13:13	4,5
20:14:15	None
27:16:16	6
16:16:16	7


<<<< (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]

0	=> [1],


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

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

1	=> [0],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 0) ]

Indx_cblk_A	indx_cblk_B



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

