#summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
+
+
= Introduction =
Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development!
+
= Multiple Sequence Alignments =
+
== Multiple Sequence Alignment Input and Output ==
=== Reading in a Multiple Sequence Alignment from a File ===
}}}
+
=== Writing a Multiple Sequence Alignment to a File ===
-== 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 (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
+ * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
# 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
+ * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
+
+=== Other Programs ===
+
+[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 ==
}}}
+----
+
= Phylogenetic Trees =
== Phylogenetic Tree Input and Output ==
Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
+
+
=== Writing of Phylogenetic Trees ===
_... to be done_
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 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 ==
}}}
+
== Pairwise Distance Based Methods ==
=== FastME ===
}}}
+
+=== PHYLIP? ===
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
= Analyzing Phylogenetic Trees =
+== PAML ==
+
+
== Gene Duplication Inference ==
_need to further test and then import GSoC 'SDI' work..._