Edited wiki page PhyloBioRuby through web user interface.

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 503fc75..ab6faf9 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -43,6 +43,32 @@ msa.each do |entry|
 end
 }}}
 
+Blah
+{{{
+# Reads in a Fasta-formatted multiple sequence alignment (which does
+# not have to be aligned, though) and stores its sequences in
+# array 'seq_ary'.
+seq_ary = Array.new
+fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
+fasta_seqs.entries.each do |seq|
+  seq_ary.push( seq )
+end
+
+# Creates a multiple sequence alignment (possibly unaligned) named
+# 'seqs' from array 'seq_ary'.
+seqs = Bio::Alignment.new( seq_ary )
+seqs.each { |seq| puts seq.to_s }
+
+
+puts seqs.consensus
+
+# Writes multiple sequence alignment (possibly unaligned) 'seqs'
+# to a file in phylip format.
+File.open('out1.phylip', 'w') do |f|
+  f.write(seqs.output(:phylip))
+end
+}}}
+
 Relevant API documentation:
 
  * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report]