class Bio::PAML::Yn00

Description

Bio::PAML::Yn00 is a wrapper for running PAML yn00 program.

Because most of the methods in this class are inherited from Bio::PAML::Common, see documents of Bio::PAML::Common for details.

Examples

Example 1:

require 'bio'
# Reads multi-fasta formatted file and gets a Bio::Alignment object.
alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat,
                               'example.fst').alignment
# Creates a Yn00 object
baseml = Bio::PAML::Yn00.new
# Sets parameters
baseml.parameters[:verbose] = 1
baseml.parameters[:icode] = 0
# You can also set many parameters at a time.
baseml.parameters.update({ :weighting => 0, :commonf3x4 => 0 })
# Executes yn00 with the alignment
report = yn00.query(alignment)