Common
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.
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)
Default parameters when running baseml.
The parameters whose values are different from the baseml defalut value (described in pamlDOC.pdf) in PAML 4.1 are:
seqfile, outfile, treefile, ndata, noisy, verbose
Default program name
Generated with the Darkfish Rdoc Generator 2.