From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Feb 2011 08:29:47 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7f6a904694d29b48334c4dc6fcc25c9f76966cc5;p=jalview.git

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

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index b6fecdf..c5f1cb3 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 =
@@ -20,7 +20,7 @@ require 'bio'
 
 == Calculating a Multiple Sequence Alignment  ==
 
-BioRuby! can be used to execute a variety of 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.
 
@@ -84,13 +84,30 @@ require 'bio'
 }}}
 
 
-= Phylogenetic Inference =
+= Phylogenetic Trees =
+
+== Reading and Writing of Phylogenetic Trees ==
+
+*... to be done*
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
+
+
+== Phylogenetic Inference ==
+
+*Currently !BioRuby does not contain any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.*
 
 == Maximum Likelihood ==
 
 === RAxML ===
 
-... to be done
+*... to be done*
 
 {{{
 #!/usr/bin/env ruby
@@ -110,3 +127,4 @@ require 'bio'
 require 'bio'
 
 }}}
+