|first line||the number of tips, the number of characters|
|subsequent lines||offspring name, parent name, branch length, character state(s).|
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.
Bio::Phylo::IO The pagel unparser is called by the Bio::Phylo::IO object. Look there to learn how to create pagel formatted files. Bio::Phylo::Manual Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>.
If you use Bio::Phylo in published research, please cite it:
<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>
|perl v5.20.3||BIO::PHYLO::UNPARSERS::PAGEL (3)||2014-02-08|