Edited wiki page PhyloBioRuby through web user interface.

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 = Introduction =
 
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+Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development!
 
 
-= Details =
+= Multiple Sequence Alignments =
 
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-  * Text in *bold* or _italic_
-  * Headings, paragraphs, and lists
-  * Automatic links to other wiki pages
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+== Multiple Sequence Alignment Input and Output ==
+
+=== 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'
+
+}}}
+
+
+
+== 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
+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)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+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 ===
+
+{{{
+#!/usr/bin/env ruby
+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)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+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 ==
+
+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..._
+
+
+== Others? ==
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