X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=b6fecdfbe99e0862d6155bb23e095fca440b331a;hb=bad38a9477399e99828c53dc59aceaf2b8141690;hp=bfb1c4cbc822b8c032214b962c56010d616eeba9;hpb=4fb2be47b1fcf014f2e3f327e69833a458b99c4d;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index bfb1c4c..b6fecdf 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -2,7 +2,7 @@
 
 = Introduction =
 
-Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!.
+Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
 
 
 = Multiple Sequence Alignments =
@@ -11,21 +11,102 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby --
 
 ... 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('/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 }
+#
+}}}
+
+=== 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 =
 
-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
+== 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'
+
+}}}