== Multiple Sequence Alignment Input and Output ==
-=== Reading in a Multiple Sequence Alignments from a File ===
+=== Reading in a Multiple Sequence Alignment from a File ===
_... to be done_
-== Calculating Multiple Sequence Alignments ==
+== 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]).
+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.
# and stores the result in 'report'.
options = ['--maxiterate', '1000', '--localpair']
mafft = Bio::MAFFT.new('path/to/mafft', options)
-report = mafft.query_align( seqs)
+report = mafft.query_align(seqs)
# Accesses the actual alignment
align = report.alignment
# Prints each sequence to the console.
-report.align.each { |s| puts s.to_s }
-#
+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 ===
# and stores the result in 'report'.
options = ['-quiet', '-maxiters', '64']
muscle = Bio::Muscle.new('path/to/muscle', options)
-report = muscle.query_align( seqs)
+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 }
-#
+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 ==
== Phylogenetic Inference ==
-*Currently !BioRuby does not contain any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.*
+_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 ==
}}}
+=== PHYLIP? ===
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
= Analyzing Phylogenetic Trees =
+== PAML ==
+
== Gene Duplication Inference ==
_need to further test and then import GSoC 'SDI' work..._