Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

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-#summary One-sentence summary of this page.
+#summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
 
 = Introduction =
 
-Add your content here.
+Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
 
 
-= Details =
+= Multiple Sequence Alignments =
 
-Add your content here.  Format your content with:
-  * Text in *bold* or _italic_
-  * Headings, paragraphs, and lists
-  * Automatic links to other wiki pages
\ No newline at end of file
+== Reading in a Multiple Sequence Alignment from a File ==
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+== Calculating a Multiple Sequence Alignment  ==
+
+BioRuby! can be used to execute a variety of multiple sequence alignment
+programs (such as [http://mafft.cbrc.jp/alignment/software/ MAFFT], [http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], [http://www.drive5.com/muscle/ Muscle]). 
+In the following, examples for using the MAFFT and Muscle are shown.
+
+=== MAFFT ===
+
+
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Calculates the alignment using the MAFFT program 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)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+report.align.each { |s| puts s.to_s }
+#
+}}}
+
+=== Muscle ===
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Calculates the alignment using the Muscle program on the local
+# machine with options '-quiet -maxiters 64'
+# 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 }
+#
+}}}
+
+
+== Manipulating Multiple Sequence Alignment  ==
+
+It is probably a good idea to 'clean up' multiple sequence to be used
+for phylogenetic inference. For instance, columns with more than 50% gaps can be deleted, like so:
+
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+= Phylogenetic Inference =
+
+== Maximum Likelihood ==
+
+=== RAxML ===
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+== Pairwise Distance Based Methods ==
+
+=== FastME ===
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}