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Author image Rutger Vos
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Bio::Phylo::Parsers::Figtree - Parser used by Bio::Phylo::IO, no serviceable parts inside


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:


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.


There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.


The figtree parser is called by the Bio::Phylo::IO object. Look there to learn how to parse phylogenetic data files in general.


Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com


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