| Bio::Phylo::Unparsers::Pagel - Serializer used by Bio::Phylo::IO, no serviceable parts inside |
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 the Bio::Phylo::IO manpage object, so look there to learn about parsing and serializing in general.
The pagel unparser is called by the the Bio::Phylo::IO manpage object. Look there to learn how to create pagel formatted files.
Also see the manual: the Bio::Phylo::Manual manpage and http://rutgervos.blogspot.com.
$Id: Pagel.pm 843 2009-03-04 23:50:27Z rvos $
| Bio::Phylo::Unparsers::Pagel - Serializer used by Bio::Phylo::IO, no serviceable parts inside |