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

query(alignment) click to toggle source

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:

Returns

Report object

Calls superclass method Bio::PAML::Common#query 
   # File lib/bio/appl/paml/yn00.rb
83 def query(alignment)
84   super(alignment)
85 end
query_by_string(alignment = nil) click to toggle source

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:

Returns

Report object

Calls superclass method Bio::PAML::Common#query_by_string 
   # File lib/bio/appl/paml/yn00.rb
97 def query_by_string(alignment = nil)
98   super(alignment)
99 end