Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index dfb8ed2..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.
 
 
@@ -50,14 +50,14 @@ require 'bio'
 # and stores the result in 'report'.
 options = ['--maxiterate', '1000', '--localpair']
 mafft = Bio::MAFFT.new('path/to/mafft', options)
-report = mafft.query_align( seqs)
+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 }
-#
+align.each { |s| puts s.to_s }
+
 }}}
 
 References:
@@ -79,14 +79,14 @@ require 'bio'
 # and stores the result in 'report'.
 options = ['-quiet', '-maxiters', '64']
 muscle = Bio::Muscle.new('path/to/muscle', options)
-report = muscle.query_align( seqs)
+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 }
-#
+align.each { |s| puts s.to_s }
+
 }}}
 
 References:
@@ -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..._