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.
| 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;