<<<<< 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 = 70 ,
#{Sites in the segment}_rec = 65 .


<< 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        TA-CATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCATG--------------------
seq0001        TA-CATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCATG--------------------
seq0002        TA-CATCTTAGAAGGTGCGTCCTGTCAGTTAGCATCCGTG--------------------
seq0003        TA-CATCTTA-AAGGTTCGTCCTGTCAGTTAGCATCCGTG--------------------
seq0004        TA-CATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCGTG--------------------
seq0005        TA-CAGCTTAGAAGGTATGTCCTGTCAGTTAGCATCCATG--------------------
seq0006        TT-CATCTTATAAGGTTCGTCCTGTCAGTTAGAATCCATG--------------------
seq0007        TA-CATCTTATAAGGTTCATCCTGTCAGTTAGCTTCCATG--------------------
seq0008        AA-CATCTTAATAAGTTCGTTC--------------------------------------
seq0009        TA-CATCTTATAATGCTCGCCCTGTCAGTTAACTTACCTG--------------------
seq0013        TA-TATCTGC--TTGTTGCTCCGGTCGG---A-TGCCATGAATCCCCACACCTACTTAAA
seq0014        TA-AATCATCATTTTGTCGTACTGTCATTTAGGTTCCAAG--------------------
seq0015        -A-C------------------------TTAGCTTCCATG--------------------
seq0018        TG-TGTCCTCACATGTTCGTTCTGTCGTTTAGCTTCCATG--------------------
seq0020        TCACCTCTTCAAATGTTGGTCGTGGCAGTTTGCTTGAATG--------------------

(position)     6666666666
               0123456789
                         
seq0000        -----CCCTA
seq0001        -----CCCTA
seq0002        -----CCCTA
seq0003        -----CCCTA
seq0004        -----CCCTA
seq0005        -----CCGTA
seq0006        -----CCGTA
seq0007        -----CCGTA
seq0008        -------CTA
seq0009        ------ACT-
seq0013        CTGGC-ACAA
seq0014        ------ACTA
seq0015        ------ACTA
seq0018        ------ACGA
seq0020        ------ACTA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        T-ACATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCATGCC------------------
seq0001        T-ACATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCATGCC------------------
seq0002        T-ACATCTTAGAAGGTGCGTCCTGTCAGTTAGCATCCGTGCC------------------
seq0003        T-ACATCTTA-AAGGTTCGTCCTGTCAGTTAGCATCCGTGCC------------------
seq0004        T-ACATCTTAGAAGGTTCGTCCTGTCAGTTAGCATCCGTGCC------------------
seq0005        T-ACAGCTTAGAAGGTATGTCCTGTCAGTTAGCATCCATGCC------------------
seq0006        T-TCATCTTATAAGGTTCGTCCTGTCAGTTAGAATCCATGCC------------------
seq0007        T-ACATCTTATAAGGTTCATCCTGTCAGTTAGCTTCCATGCC------------------
seq0008        A-ACATCTTAATAAGTTCGTTC--------------------------------------
seq0009        T-ACATCTTATAATGCTCGCCCTGTCAGTTAACTTACCTGAC------------------
seq0013        T-ATATCT--GCTTGTTGCTCCGGTCGGATGCCATGAATCCCCACACCTACTTAAACTGG
seq0014        T-AAATCATCATTTTGTCGTACTGTCATTTAGGTTCCAAGAC------------------
seq0015        A--------------------------CTTAGCTTCCATGAC------------------
seq0018        T-GTGTCCTCACATGTTCGTTCTGTCGTTTAGCTTCCATGAC------------------
seq0020        TCACCTCTTCAAATGTTGGTCGTGGCAGTTTGCTTGAATGAC------------------

(position)     66666
               01234
                    
seq0000        --CTA
seq0001        --CTA
seq0002        --CTA
seq0003        --CTA
seq0004        --CTA
seq0005        --GTA
seq0006        --GTA
seq0007        --GTA
seq0008        --CTA
seq0009        ----T
seq0013        CACAA
seq0014        ---TA
seq0015        ---TA
seq0018        ---GA
seq0020        ---TA


<<<<< 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, -5) .

[ 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    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0001   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0002   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0003   	    0    -    1    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0004   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0005   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0006   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0007   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -25  -25    -    -    -    -    -    -    -    -
seq0008   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -26  -26    -    -    -    -    -    -    -    -
seq0013   	    0    -    1    0    0    0    0    0    -    -    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4
seq0014   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -26  -26    -    -    -    -    -    -    -    -
seq0015   	   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   24    0    0    0    0    0    0    0    0    0    0    0    0  -26  -26    -    -    -    -    -    -    -    -
seq0018   	    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -26  -26    -    -    -    -    -    -    -    -
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  -26  -26    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4
seq0013   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5   -5   -5   -5
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5



<<<<< 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	23	8	-1	n/a	12
1	2	2	27	14	1	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13
2	10	11	20	15	2	n/a	10
3	27	27	23	16	24	n/a	12
4	28	28	20	7	-3	n/a	10
5	29	64	20	6,4	-4,-5	0	10
6	40	41	15	1	-25	n/a	0,1,2,3,4,5,6,7
7	40	41	29	0	-26	n/a	9,11,12,13,14
8	62	64	19	3	-5	n/a	0,1,2,3,4,5,6,7,8
9	63	64	29	2	-5	n/a	11,12,13,14
10	64	64	17	5	-4	n/a	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	2	0	0	0	0	0
5	2	1	0	0	0	0
6	1	0	0	0	0	0
7	1	1	0	0	0	0
8	0	0	0	1	0	0
9	0	0	0	1	0	0
10	1	1	0	0	0	0


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


[ 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	Complex(???)	23:0:0:X	23:2:26:X
1	0	1	1	Shift	28:2:2:-	28:1:1:-
2	0	2	2	Shift	20:10:11:X	20:8:9:X
3	0	1	1	Complex(???)	23:4:27:X	23:2:26:X
4	0	1	1	Complex(???)	20:28:30:X/20:32:32:X	None
5	0	37	36	Complex(???)	20:32:32:X/20:40:64:-	20:42:61:-
6	0	2	2	Complex(???)	15:65:65:-	None
7	0	2	2	Complex(???)	16:22:66:X	16:22:41:X
8	0	3	3	NO_ASSOCIATED_EVENT(???)	None	25:62:62:-
9	0	2	2	NO_ASSOCIATED_EVENT(???)	None	25:62:62:-
10	0	1	1	Complex(???)	17:69:69:X	17:62:63:X


[ Contents of %indel_ref2assoc_cblks ]

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

23:0:0	0
28:2:2	1
23:4:27	3
20:10:11	2
5:10:10	{Equivalent to '5:10:10'(rec)}
16:22:66	7
20:28:30	4
20:32:32	4,5
20:40:64	5
15:65:65	6
17:69:69	10


[ Contents of %indel_rec2assoc_cblks ]

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

28:1:1	1
23:2:26	0,3
20:8:9	2
5:10:10	{Equivalent to '5:10:10'(ref)}
16:22:41	7
20:42:61	5
25:62:62	8,9
23:62:62	None
21:62:62	None
17:62:63	10


<<<< (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]

9	=> [8],


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

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

8	=> [9],


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

Indx_cblk_A	indx_cblk_B

0	3
4	5


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

[ For the 1 th pair: (0, 3) ]


{ The representative path is: 0  -> 3 }


( 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)	0	0	-1	-1	23	12	12
2nd(reconstructed)	27	27	24	24	23	12	12


( 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	23:0:0:X	23:2:2:X
2nd(reconstructed)	Merge(same-type)	23:2:2:X/23:4:27:X	23:2:26:X


[ For the 2 th pair: (4, 5) ]


{ The representative path is: 4  -> 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)	28	28	-3	-3	20	10	10
2nd(reconstructed)	29	64	-4	-5	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)	Merge(same-type)	20:28:30:X/20:32:32:X	20:29:32:X
2nd(reconstructed)	Complex	20:29:32:X/20:66:69:-/20:42:61:-	20:42:61:-


