Bio::Phylo::Parsers::Fastnexus - Parses nexus files. No serviceable parts inside.


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, spaces in single quoted strings are replaced with underscores, private nexus blocks (and the 'assumptions' block) are skipped. It currently doesn't handle 'interleaved' matrices and 'mixed' data.



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


Also see the manual: Bio::Phylo::Manual.


CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below):


Please report any bugs or feature requests to, or through the web interface at I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id:,v 1.4 2006/04/12 22:38:23 rvosa Exp $


Rutger A. Vos,

web page:


The author would like to thank Jason Stajich for many ideas borrowed from BioPerl, and CIPRES and FAB* for comments and requests.


Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.