From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Feb 2011 08:35:37 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ff39f35fbb20f2610af44c2b7bc45d29f4bfa80b;p=jalview.git

Edited wiki page PhyloBioRuby through web user interface.
---

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index c5f1cb3..45c0d5f 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -7,7 +7,7 @@ Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -
 
 = Multiple Sequence Alignments =
 
-== Reading in a Multiple Sequence Alignment from a File ==
+== Reading in Multiple Sequence Alignments from Files ==
 
 ... to be done
 
@@ -18,15 +18,26 @@ require 'bio'
 }}}
 
 
-== Calculating a Multiple Sequence Alignment  ==
+== Writing Multiple Sequence Alignments to Files ==
+
+... to be done
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+
+== Calculating Multiple Sequence Alignments  ==
 
 !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 ===
-
 
+=== MAFFT ===
 
 {{{
 #!/usr/bin/env ruby
@@ -47,6 +58,7 @@ report.align.each { |s| puts s.to_s }
 #
 }}}
 
+
 === Muscle ===
 
 {{{
@@ -69,7 +81,7 @@ report.align.each { |s| puts s.to_s }
 }}}
 
 
-== Manipulating Multiple Sequence Alignment  ==
+== Manipulating Multiple Sequence Alignments  ==
 
 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:
@@ -128,3 +140,12 @@ require 'bio'
 
 }}}
 
+
+= Analyzing Phylogenetic Trees =
+
+== Gene Duplication Inference ==
+
+*Need to further test and then import GSoC 'SDI' work.*
+
+
+== Others? ==