X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=f44e59b1aecfa51ad2b55dbcf38dc2c88180d2a1;hb=fe6161f9ff04df6aad319a34d0d5d3d312cf77e5;hp=5b6ac60084bac49a7ef01db6570ebd5279abb84e;hpb=69e816b09597dc4c6e50bd345a26a469db4830b4;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 5b6ac60..f44e59b 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -7,7 +7,9 @@ Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -
 
 = Multiple Sequence Alignments =
 
-== Reading in a Multiple Sequence Alignments from a File ==
+== Multiple Sequence Alignment Input and Output ==
+
+=== Reading in a Multiple Sequence Alignment from a File ===
 
 _... to be done_
 
@@ -18,7 +20,7 @@ require 'bio'
 }}}
 
 
-== Writing a Multiple Sequence Alignment to a File ==
+=== Writing a Multiple Sequence Alignment to a File ===
 
 _... to be done_
 
@@ -30,10 +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.
 
 
@@ -46,18 +48,25 @@ require 'bio'
 # Calculates the alignment using the MAFFT program on the local
 # machine with options '--maxiterate 1000 --localpair'
 # and stores the result in 'report'.
-options = [ '--maxiterate', '1000', '--localpair' ]
-mafft = Bio::MAFFT.new('path/to/mafft', options )
-report = mafft.query_align( seqs)
+options = ['--maxiterate', '1000', '--localpair']
+mafft = Bio::MAFFT.new('path/to/mafft', options)
+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:
+
+ * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298 
+
+ * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900 
+
+
 
 === Muscle ===
 
@@ -68,18 +77,21 @@ require 'bio'
 # Calculates the alignment using the Muscle program on the local
 # machine with options '-quiet -maxiters 64'
 # and stores the result in 'report'.
-options = [ '-quiet', '-maxiters', '64' ]
-muscle = Bio::Muscle.new('path/to/muscle', options )
-report = muscle.query_align( seqs)
+options = ['-quiet', '-maxiters', '64']
+muscle = Bio::Muscle.new('path/to/muscle', options)
+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:
+
+ * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
 
 == Manipulating Multiple Sequence Alignments ==
 
@@ -98,7 +110,21 @@ require 'bio'
 
 = Phylogenetic Trees =
 
-== Reading and Writing of Phylogenetic Trees ==
+== Phylogenetic Tree Input and Output ==
+
+=== Reading in of Phylogenetic Trees ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
+
+=== Writing of Phylogenetic Trees ===
 
 _... to be done_
 
@@ -113,7 +139,9 @@ Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_do
 
 == 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.*
+_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 ==
 
@@ -140,9 +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..._