class Bio::Tcoffee

Bio::Tcoffee is a wrapper class to execute t-coffee.

Please refer documents in bio/apple/tcoffee.rb for references.

Constants

DEFAULT_PARSER

CLUSTAL W result data (*.aln file) parser class.

DEFAULT_PROGRAM

default program name

Private Instance Methods

_option_input_file(fn) click to toggle source

generates options specifying input filename. returns an array of string

   # File lib/bio/appl/tcoffee.rb
38 def _option_input_file(fn)
39   [ '-infile', fn ]
40 end
_option_output_dndfile(fn) click to toggle source

generates options specifying output filename. returns an array of string

   # File lib/bio/appl/tcoffee.rb
50 def _option_output_dndfile(fn)
51   [ '-newtree', fn ]
52 end
_option_output_file(fn) click to toggle source

generates options specifying output filename. returns an array of string

   # File lib/bio/appl/tcoffee.rb
44 def _option_output_file(fn)
45   [ '-outfile', fn ]
46 end