Bio::Phylo::Unparsers::Pagel - Serializer used by Bio::Phylo::IO, 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:
the number of tips, the number of characters
offspring name, parent name, branch length, character state(s).
Here is an example of what the output might look like:
4 2 A,n1,0.000000,1,2 B,n1,0.000000,1,2 n1,n2,0.000000 C,n2,0.000000,2,2 n2,n3,0.000000 D,n3,0.000000,2,1
To the unparse() function pass a tree object as value of the '-phylo' argument. The tips in this tree must be linked to taxon objects, and the taxon objects must be linked to datum objects whose character state sequences are to be serialized.
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 about parsing and serializing in general.
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 and http://rutgervos.blogspot.com.
$Id: Pagel.pm 1235 2010-03-02 16:11:07Z rvos $
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.