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):


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 1.19 2005/09/29 20:31:18 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.