Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

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 = Introduction =
 
-Add your content here.
+Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!.
+
+
+= Multiple Sequence Alignments =
+
+== Reading in a Multiple Sequence Alignment from a File ==
+
+... to be done
+
+== Calculating a Multiple Sequence Alignment  ==
+
+=== MAFFT ===
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+options = [ '--maxiterate', '1000', '--localpair' ]
+mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
+report = mafft.query_align( seqs)
+}}}
 
 
-= Details =
 
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