From 8ace8ed9c6cf72b4e3bfd613f2224c8d201ea040 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 07:56:48 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index bfb1c4c..204edf0 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -18,9 +18,19 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- {{{ #!/usr/bin/env ruby require 'bio' + +# Calculates the alignment using the MAFFT program +# on the local machine, and stores the result in 'report'. options = [ '--maxiterate', '1000', '--localpair' ] -mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options ) +mafft = Bio::MAFFT.new('path/to/mafft', options ) report = mafft.query_align( seqs) + +# Accesses the actual alignment +align = report.alignment + +# Prints each sequence to the console. +report.align.each { |s| puts s.to_s } +# }}} -- 1.7.10.2