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:
- first line
the number of tips, the number of characters
- subsequent lines
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.
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The pagel unparser is called by the Bio::Phylo::IO object. Look there to learn how to create pagel formatted files.
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