From 24a5e3936f8b53b844701f5d7531eab5fcf23bd3 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 08:03:59 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 204edf0..020d6a2 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -13,14 +13,22 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- == Calculating a Multiple Sequence Alignment == +BioRuby can be used to execute a variety of multiple sequence alignment +programs (such as MAFFT, Probcons, ClustalW, Muscle). +In the following, examples for using the MAFFT and + === MAFFT === + + {{{ #!/usr/bin/env ruby require 'bio' # Calculates the alignment using the MAFFT program -# on the local machine, and stores the result in 'report'. +# on the local machine with options +# '--maxiterate', '1000', '--localpair' +# and stores the result in 'report'. options = [ '--maxiterate', '1000', '--localpair' ] mafft = Bio::MAFFT.new('path/to/mafft', options ) report = mafft.query_align( seqs) @@ -33,7 +41,25 @@ report.align.each { |s| puts s.to_s } # }}} +=== Muscle === + + +#!/usr/bin/env ruby +require 'bio' + +# Calculates the alignment using the MAFFT program +# on the local machine, and stores the result in 'report'. +options = [ '-quiet', '-maxiters', '64' ] +muscle = Bio::Muscle.new('path/to/muscle', options ) +report = muscle.query_align( seqs) + +# Accesses the actual alignment +align = report.alignment +# Prints each sequence to the console. +report.align.each { |s| puts s.to_s } +# + Add your content here. Format your content with: * Text in *bold* or _italic_ -- 1.7.10.2