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#NEXUS
[ NEXUS test file. Weird, but NEXUS standard compatible.]
begin data;
dimensions ntax=9 nchar=48;
format datatype=dna gap=- missing=? interleave=yes;
options gapmode=newstate;
taxlabels t1
't2 the name'
'isn''that [a] strange name?' 'one should be punished, for (that)!'
t5 t6 t7 t8 t9;
charlabels 1 'a', 2 'b', 3 'c', 5 'f', 10 'A', 11 'B', 23 'x', 24 'y', 30 '1,2,3 can''t decide for a name?!', 48 final;
matrix
[interleaved matrix: secont taxon name is spelled either with quotes or with underscores,
but must be treated as the same name]
t1 A-C-G-Tc-gtgtgtgctct-t-t
't2 the name' A-C-GcTc-gtg-----tct-t-t
'isn''that [a] strange name?' A-CcGcTc-gtgtgtgct------
'one should be punished, for (that)!' A-C-G-T-----------------
t5 A-C?G-T?--acgt??-???-???
t6 AcCaGtTc-?--aaaaaaaa-a-a
t7 A?C-GgTg-ggggggggggg-g-g
t8 AtCtGtTt-ttttttttttt-?-?
[last taxon of the matrix]
t9 cccccccc-cccccccccccNc-c
t1 ------ac-gtgtgtgctct-t-t
t2_the_name ----acac-gtg-----tct-t-t
'isn''that [a] strange name?' --acacac-gtgtgtgct------
'one should be punished, for (that)!' ------------------------
t5 --??---?--acgt??-???-???
t6 acgactac-?--aaaaaaaa-a-a
t7 ??--?ggg-ggggggggggg-g-g
t8 tttttttt-ttttttttttt-?-?
[last taxon of the matrix]
t9 cccccccc-cccccccccccNc-c
;
end;
[t5 --??---?--a[last quarter of sequence starts here]cgt??-???-???]
[ this is a [nested ] comment]
[ a special commend was [& not cut out] here]
begin sets;
[simple blocks dividing the data into three parts]
charset
c1=1-8;
charset c2= 9-16;
charset c3
=
17-24
;
[characters can be specified by their character labels]
charset byname= 1 f-'1,2,3 can''t decide for a name?!';
charset pos1=1-48\3;
charset pos2=b-final\3;
charset pos3=3-11\3 12-48\3;
charset mix=pos2 1; charset mux=mix 9 c3
;
[big chinks are nice for testing]
charset bigchunk=2-47;
charset firsthalf=1-24;
charset secondhalf=25-48;
charset big=1 3 5 7;
[classical subdivision into codon positions]
charpartition codons = a : pos1,
b: pos2 ,
c:pos3
;
[some taxon sets]
taxset normal=1 3 4-6 8;
taxset tbyname1=3 t1-t6;
taxset tbyname2 = 't2 the_name' - t7;
taxset tbyname3 = t1 - t2_the_name;
taxset reference=1 2 tbyname1;
[another character partition]
charpartition
part=one:c1,
two:c2,
three:c3;
[and a taxpartition]
taxpartition taxpart=goodnames:1 5-9, badnames: 2 3 4;
end;
[unknown blocks should be read and ignored]
begin spam;
this is a unknown block;
and should be completely ignored;
end;
[Some trees]
begin trees;
translate
3 t1,
4 't2 the name'
,1 'isn''that [a] strange name?',
2 'one should be punished, for (that)!'
,
9 t5,
7 t6 ,
8 t7,
5
t8, 6 t9;
tree tree1 = [&R] [&W3.5] (1,(2,3),(4,(5,6,(7,(8,9)))));
tree tree1 = (1,(2,(4,(5,6,(7,(8,(9,3)))))));
tree tree1 = (1,(2:0.5,(4:0.3,(5:1.2,6:3.4,(7:1,(8:99.9,(9:99,3:0.98)12:13)33:0.44)1:2.0)3:4.0)0.3:0.4)10:100);
end;
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