Bio::Phylo::Unparsers::Pagel - Unparses pagel data files. No serviceable parts inside.
This module unparses a Bio::Phylo data structure into an input file for Discrete/Continuous/Multistate. The pagel file format (as it is interpreted here) consists of:
- first line
the number of tips, the number of characters
- subsequent lines
offspring name, parent name, branch length, character state(s).
During unparsing, the tree is randomly resolved, and branch lengths are formatted to %f floats (i.e. integers, decimal point, integers).
The pagel module is called by the Bio::Phylo::IO object, so look there to learn how to create Pagel formatted files.
The pagel unparser is called by the Bio::Phylo::IO object. Look there to learn how to create pagel formatted files.
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): http://www.cpanforum.com/dist/Bio-Phylo
Please report any bugs or feature requests to
firstname.lastname@example.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. 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: Pagel.pm,v 1.19 2005/09/29 20:31:18 rvosa Exp $
Rutger A. Vos,
- web page: http://www.sfu.ca/~rvosa/
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar 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.