+====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.
+