Author: Rutger Vos
Description: NeXML is a file format for encoding phyloinformatic data using XML.
Keywords: NeXML, XML, NEXUS, phyloinformatics, phylogenetics, phylogenies, trees, dna, rna, nucleotide, standard, continuous, amino, acid, matrix, tree, network, data

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# FAIL

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# [NeXML]

Rich phyloinformatic data

## The future data exchange standard is here!

NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Process nexml data

### FAIL

~ / nexml / nex2xml
| Last updated: Thu Aug 25 05:35:56 EDT 2011 —

### Detailed results

Below are the messages received from the parsing and validation operations (if any). They are organized as debugging messages (), informational (), warnings (), errors () and fatal exceptions ():

- going to parse nexus data
- going to split nexus data on lines
- going to split lines on tokens
- going to split non-quoted/commented fragments on whitespace
- tokenized and split data, going to parse blocks
- found nexus token
- starting taxa block
- number of taxa: 6
- starting taxlabels
- starting characters block
- number of characters: 45
- datatype: dna
- missing character: ?
- gap character: -
- block has title 'dna_forty_five'
- charlabels: labone labtwo labthree labfour labfive labsix labseven
- adding matrix metadata
- Can't call method "set_name" on an undefined value at perl/lib/Bio/Phylo/Matrices/Matrix.pm line 431, <DATA> line 1.

### Submitted contents

Below are the contents (if any) that were submitted to this query:

1 #nexus
2
3 begin taxa;
4 dimensions ntax=6;
5 taxlabels
6 'P. fimbriata'
7 'P. robusta'
8 'P. americana'
9 'P. myriophylla'
10 'P. polygama'
11 'P. macrophylla'
12 ;
13 blockid bogus;
14 end;
15
16 [!
17 *************
18 * dna *
19 *************
20 ]
21 begin characters;
22 dimensions nchar=45;
23 format datatype=dna missing=? gap=-;
24 title dna_forty_five;
25 CHARLABELS labone labtwo labthree labfour labfive labsix labseven;
26
27 matrix
28 P._fimbriata {a, G}cctcggcttaacgaacctcggcttaacgaacctcggcttaacga
29 P._robusta (a, , C)cctcggcttaaccaacctcggcttaacgaacctcggcttaacga
30 P._americana rcgtcgctttca---acgtcgctttcaccaacgtcgctttcacca
31 P._myriophylla acgtcgctttca---acgtcgctttcaccaacgtc?ctttcacca
32 P._polygama acgtcgctctcaccaacgtcgctttcaccaacgtc?ctttcacca
33 P._macrophylla acgtcgctctcaccaacgtcgctttcaccaacgtcgctttcacca
34 ;
35 end;
36 BEGIN SETS;
37 CHARSET csone (STANDARD CHARACTERS='dna forty five') = 1-3;
38 CHARSET cstwo (CHARACTERS='dna forty five' STANDARD) = csone;
39 CHARSET csthree = 5 labfour cstwo;
40 CHARSET csfour = 4 labone - . \ 3 7;
41 CHARSET csfive = 44 43 csthree 41 10 - 16 \2 18 40 42 45;
42 CHARSET cssix (CHARACTERS='dna forty five') = labseven csthree csfour 6;
43 end;
44
45
46 BEGIN ASSUMPTIONS;
47
48 EXSET csone (STANDARD CHARACTERS='dna forty five') = 1-3;
49 EXSET cstwo (CHARACTERS='dna forty five' STANDARD) = csone;
50 EXSET csthree = 5 labfour cstwo;
51 EXSET * csfour = 4 labone - . \ 3 7;
52 EXSET csfive = 44 43 csthree 41 10 - 16 \2 18 40 42 45;
53 EXSET cssix (CHARACTERS='dna forty five') = labseven csthree csfour 6;
54 end;