= Introduction =
-Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
+Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development!
= Multiple Sequence Alignments =
-== Reading in a Multiple Sequence Alignment from a File ==
+== Multiple Sequence Alignment Input and Output ==
-... to be done
+=== Reading in a Multiple Sequence Alignment from a File ===
+
+_... to be done_
{{{
#!/usr/bin/env ruby
}}}
-== Calculating a Multiple Sequence Alignment ==
+=== Writing a Multiple Sequence Alignment to a File ===
-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]).
-In the following, examples for using the MAFFT and Muscle are shown.
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
-=== MAFFT ===
+== 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], 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.
+
+
+=== MAFFT ===
{{{
#!/usr/bin/env ruby
# Calculates the alignment using the MAFFT program on the local
# machine with options '--maxiterate 1000 --localpair'
# and stores the result in 'report'.
-options = [ '--maxiterate', '1000', '--localpair' ]
-mafft = Bio::MAFFT.new('path/to/mafft', options )
-report = mafft.query_align( seqs)
+options = ['--maxiterate', '1000', '--localpair']
+mafft = Bio::MAFFT.new('path/to/mafft', options)
+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 ===
{{{
# 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)
+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 }
-#
+align.each { |s| puts s.to_s }
+
}}}
+References:
-== Manipulating Multiple Sequence Alignment ==
+ * 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 ==
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
+_... to be done_
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+}}}
+
+
+= 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
}}}
+Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
-= Phylogenetic Inference =
+
+== 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
+_... to be done_
{{{
#!/usr/bin/env ruby
=== FastME ===
-... to be done
+_... 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..._
+
+
+== Others? ==
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git://source.jalview.org / jalview.git / blobdiff