+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+report.align.each { |s| puts s.to_s }
+#
+}}}
+
+=== 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.
+report.align.each { |s| puts s.to_s }
+#
+}}}
+
+
+== Manipulating Multiple Sequence Alignment ==
+
+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 Inference =
+
+== Maximum Likelihood ==
+
+=== RAxML ===
+
+... to be done