X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=wiki%2FPhyloBioRuby.wiki;h=9972a5160a83817098f72ed1a02536e9ebcc9a6c;hb=dc7b38fb200e01f848623762f52bf345b51dad1d;hp=bd95112e9400d3f7fdbc7cedd1362047df41a3ac;hpb=fca1f78160ec8e8fd7b7a08e41a54c140aef058f;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index bd95112..9972a51 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -1,25 +1,50 @@
 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
 
+
+
 = 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 =
 
-== Reading in a Multiple Sequence Alignment from a File ==
 
-... to be done
+== Multiple Sequence Alignment Input and Output ==
 
-== Calculating a Multiple Sequence Alignment  ==
+=== Reading in a Multiple Sequence Alignment from a File ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+ 
+
+=== Writing a Multiple Sequence Alignment to a File ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
 
-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.drive5.com/muscle/ ClustalW], [http://www.drive5.com/muscle/ Muscle]). 
-In the following, examples for using the MAFFT and Muscle are shown.
 
-=== MAFFT ===
 
+== 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], 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.
+
+
+=== MAFFT ===
 
 {{{
 #!/usr/bin/env ruby
@@ -28,18 +53,26 @@ 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 ===
 
 {{{
@@ -49,21 +82,131 @@ 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
+
+=== Other Programs ===
+
+[http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]) can be used in the same manner as the programs above. 
+
+
+== 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:
+
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
 }}}
 
 
+----
+
+= 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_
+
+{{{
+#!/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 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 ==
+
+=== RAxML ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+
+== Pairwise Distance Based Methods ==
+
+=== FastME ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+
+=== PHYLIP? ===
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
+= Analyzing Phylogenetic Trees =
+
+== PAML ==
+
+
+== Gene Duplication Inference ==
+
+_need to further test and then import GSoC 'SDI' work..._
+
 
-Add your content here.  Format your content with:
-  * Text in *bold* or _italic_
-  * Headings, paragraphs, and lists
-  * Automatic links to other wiki pages
\ No newline at end of file
+== Others? ==
\ No newline at end of file