class Bio::PAML::Baseml

Description¶ ↑

Bio::PAML::Baseml is a wrapper for running PAML baseml 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
# Reads newick tree from a file
tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').tree
# Creates a Baseml object
baseml = Bio::PAML::Baseml.new
# Sets parameters
baseml.parameters[:runmode] = 0
baseml.parameters[:RateAncestor] = 1
# You can also set many parameters at a time.
baseml.parameters.update({ :alpha => 0.5, :fix_alpha => 0 })
# Executes baseml with the alignment and the tree
report = baseml.query(alignment, tree)