+----
+
+= 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..._
+