#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;

