From bad38a9477399e99828c53dc59aceaf2b8141690 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Feb 2011 08:23:35 +0000
Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface.

---
 wiki/PhyloBioRuby.wiki |   53 +++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 48 insertions(+), 5 deletions(-)

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index bd95112..b6fecdf 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -11,10 +11,17 @@ 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.drive5.com/muscle/ ClustalW], [http://www.drive5.com/muscle/ Muscle]). 
+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 ===
@@ -62,8 +69,44 @@ 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 ==
 
-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
+=== RAxML ===
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+== Pairwise Distance Based Methods ==
+
+=== FastME ===
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
-- 
1.7.10.2