Class | Bio::PAML::Baseml |
In: |
lib/bio/appl/paml/baseml.rb
lib/bio/appl/paml/baseml/report.rb |
Parent: | 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_PROGRAM | = | 'baseml'.freeze | Default program name | |
DEFAULT_PARAMETERS | = | { # Essential argumemts :seqfile => nil, :outfile => nil, # Optional arguments :treefile => nil, :noisy => 0, :verbose => 1, :runmode => 0, :model => 5, :Mgene => 0, :ndata => 1, :clock => 0, :fix_kappa => 0, :kappa => 2.5, :fix_alpha => 1, :alpha => 0.0, :Malpha => 0, :ncatG => 5, :fix_rho => 1, :rho => 0.0, :nparK => 0, :nhomo => 0, :getSE => 0, :RateAncestor => 0, :Small_Diff => 1e-6, :cleandata => 1, :fix_blength => 0, :method => 0 |
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 |