Class | Bio::PAML::Baseml
In: | lib/bio/appl/paml/baseml.rb lib/bio/appl/paml/baseml/report.rb
Parent: | Common

## 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)

### Classes and Modules

Class Bio::PAML::Baseml::Report

### Constants

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

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