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Manual Reference Pages  -  BIO::PHYLO::PARSERS::FIGTREE (3)

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NAME

Bio::Phylo::Parsers::Figtree - Parser used by Bio::Phylo::IO, no serviceable parts inside

CONTENTS

DESCRIPTION

This module parses annotated trees in NEXUS format as produced 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.

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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::PARSERS::FIGTREE (3) 2014-02-08

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