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)
Constants
- DEFAULT_PARAMETERS
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
Default program name
Public Instance Methods
Runs the program on the internal parameters with the specified sequence alignment. Note that parameters and parameters are always modified.
For other important information, see the document of Bio::PAML::Common#query.
Arguments:
-
(required) alignment: Bio::Alignment object or similar object
- Returns
-
Report object
# File lib/bio/appl/paml/yn00.rb, line 83 def query(alignment) super(alignment) end
Runs the program on the internal parameters with the specified sequence alignment as a String object.
For other important information, see the document of query and Bio::PAML::Common#query_by_string methods.
Arguments:
-
(required) alignment: Bio::Alignment object or similar object
- Returns
-
Report object
# File lib/bio/appl/paml/yn00.rb, line 97 def query_by_string(alignment = nil) super(alignment) end