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30 Oct 2017 19:50:35 UTC
- Distribution: Bio-Phylo
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Bus factor: 1- 56.90% Coverage
- License: perl_5
- Perl: v5.8.0
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NAME
Bio::Phylo::Parsers::Figtree - Parser used by Bio::Phylo::IO, no serviceable parts inside
DESCRIPTION
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
andrate_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
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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
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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
Module Install Instructions
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm Bio::Phylo
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.