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| Bio::Phylo::Parsers::Figtree(3) | User Contributed Perl Documentation | Bio::Phylo::Parsers::Figtree(3) |
NAME
Bio::Phylo::Parsers::Figtree - Parser used by Bio::Phylo::IO, no serviceable parts insideDESCRIPTION
This module parses annotated trees in NEXUS format as interpreted by FigTree (<http://tree.bio.ed.ac.uk/software/figtree/>), i.e. trees where nodes have additional 'hot comments' attached to them in the tree description. The implementation assumes syntax as follows:
[&minmax={0.1231,0.3254},rate=0.0075583392800736]
I.e. the first token inside the comments is an ampersand, the annotations are comma-separated key/value pairs, where ranges are between curly parentheses.
The annotations are stored as meta objects, e.g.:
$node->get_meta_object('fig:rate'); # 0.0075583392800736
$node->get_meta_object('fig:minmax_min'); # 0.1231
$node->get_meta_object('fig:minmax_max'); # 0.3254
Annotations that have non-alphanumerical symbols in them will have these removed from them. For example, "rate_95%_HPD={}" becomes two annotations: "rate_95_HPD_min" and "rate_95_HPD_max".
SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.- Bio::Phylo::IO
- The figtree parser is called by the Bio::Phylo::IO object. Look there to learn how to parse phylogenetic data files in general.
- Bio::Phylo::Manual
- Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>
CITATION
If you use Bio::Phylo in published research, please cite it:Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. <http://dx.doi.org/10.1186/1471-2105-12-63>
| 2017-10-30 | perl v5.32.1 |
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