NAME

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

DESCRIPTION

This module parses nexus files. It is called by the Bio::Phylo::IO module, there is no direct usage. The parser can handle files and strings with multiple tree, taxon, and characters blocks whose links are defined using Mesquite's "TITLE = 'some_name'" and "LINK TAXA = 'some_name'" tokens.

The parser returns a reference to an array containing one or more taxa, trees and matrices objects. Nexus comments are stripped, private nexus blocks (and the 'assumptions' block) are skipped. It currently doesn't handle 'mixed' data.

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 nexus parser is called by the Bio::Phylo::IO object. Look there for examples of file parsing and manipulation.

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>