+References:
+
+ * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
+
+=== Other Programs ===
+
+_need more detail here..._
+
+[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 ==
+
+Oftentimes, multiple sequence to be used for phylogenetic inference are 'cleaned up' in some manner. For instance, some researchers prefer to delete columns with more than 50% gaps. The following code is an example of how to do that in !BioRuby.
+
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+----
+
+= Phylogenetic Trees =
+
+
+== Phylogenetic Tree Input and Output ==
+
+
+=== Reading in of Phylogenetic Trees ===
+
+
+
+====Newick or New Hampshire Format====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+====phyloXML Format====
+
+Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
+
+In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
+
+{{{
+% gem install -r libxml-ruby
+}}}
+
+This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# This creates new phyloXML parser.
+trees = Bio::PhyloXML::Parser.new('example.xml')
+
+# This prints the names of all trees in the file.
+trees.each do |tree|
+ puts tree.name
+end
+
+# If there are several trees in the file, you can access the one you wish via index.
+tree = trees[3]
+
+}}}
+
+
+====Nexus Format====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+=== Writing of Phylogenetic Trees ===
+
+====Newick or New Hampshire Format====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+====phyloXML Format====
+
+Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
+
+In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
+
+{{{
+% gem install -r libxml-ruby
+}}}
+
+This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# this creates new phyloXML writer.
+writer = Bio::PhyloXML::Writer.new('tree.xml')
+
+# Writes tree to the file "tree.xml".
+writer.write(tree1)
+
+# Adds another tree to the file.
+writer.write(tree2)
+
+
+}}}
+
+
+====Nexus Format====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+= 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..._
+
+== Optimality Criteria Based on Character Data ==
+
+Character data based methods work directly on molecular sequences and thus do not require the calculation of pairwise distances but tend to be time consuming and sensitive to errors in the multiple sequence alignment.
+
+=== Maximum Likelihood ===
+
+==== RAxML ====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+==== PhyML ====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+=== Maximum Parsimony ===
+
+Currently no direct support in !BioRuby.
+
+
+=== Bayesian Inference ===
+
+Currently no direct support in !BioRuby.
+
+
+== Pairwise Distance Based Methods ==
+
+=== Pairwise Sequence Distance Estimation ===
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+=== Optimality Criteria Based on Pairwise Distances ===
+
+
+==== Minimal Evolution: FastME ====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+=== Algorithmic Methods Based on Pairwise Distances ===
+
+==== Neighbor Joining and Related Methods ====
+
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+
+
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
+= Analyzing Phylogenetic Trees =
+
+== PAML ==
+
+
+== Gene Duplication Inference ==
+
+_need to further test and then import GSoC 'SDI' work..._
+
+
+== Others? ==
+
+
+----