Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index bebd29b..f44e59b 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -32,10 +32,10 @@ require 'bio'
 
 
 
-== Calculating Multiple Sequence Alignments  ==
+== 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]). 
+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], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]). 
 In the following, examples for using the MAFFT and Muscle are shown.
 
 
@@ -139,7 +139,9 @@ Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_do
 
 == Phylogenetic Inference ==
 
-_Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastMA..._
+_Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastME..._
+
+_What about pairwise distance calculation?_
 
 == Maximum Likelihood ==
 
@@ -166,9 +168,18 @@ require 'bio'
 
 }}}
 
+=== PHYLIP? ===
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
 
 = Analyzing Phylogenetic Trees =
 
+== PAML ==
+
 == Gene Duplication Inference ==
 
 _need to further test and then import GSoC 'SDI' work..._