#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!.
+Under development!
+
+Tutorial for multiple sequence alignments and phylogenetic methods in [http://bioruby.open-bio.org/ BioRuby].
+
+Eventually, this is expected to be placed on the official !BioRuby page.
+
+Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+
+
+Copyright (C) 2011 Christian M Zmasek
= Multiple Sequence Alignments =
-== Reading in a Multiple Sequence Alignment from a File ==
-... to be done
+== Multiple Sequence Alignment Input and Output ==
+
+=== Reading in a Multiple Sequence Alignment from a File ===
+
+The follow example shows how to read in a *ClustalW*-formatted multiple sequence alignment.
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Reads in a ClustalW-formatted multiple sequence alignment
+# from a file named "infile_clustalw.aln" and stores it in 'report'.
+report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
+
+# Accesses the actual alignment.
+align = report.alignment
+
+# Goes through all sequences in 'align' and prints the
+# actual molecular sequence.
+align.each do |entry|
+ puts entry.seq
+end
+}}}
+
+
+
+=== Writing a Multiple Sequence Alignment to a File ===
+
+
+The follow example shows how to writing a multiple sequence alignment in *FASTA*-format:
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# Creates a new file named "outfile.fasta" and writes
+# multiple sequence alignment 'align' to it in fasta format.
+File.open('outfile.fasta', 'w') do |f|
+ f.write(align.output(:fasta))
+end
+}}}
+
+The following constants determine the output format
+
+ * ClustalW: `:clustal`
+ * FASTA: `:fasta`
+ * PHYLIP interleaved (will truncate sequence names to no more than 10 characters): `:phylip`
+ * PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters): `:phylipnon`
+ * MSF: `:msf`
+ * Molphy: `:molphy`
+
+
+For example, the following writes iPHYLIP's non-interleaved format:
+
+{{{
+f.write(align.output(:phylipnon))
+}}}
+
+
+
+== 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.
-== Calculating a Multiple Sequence Alignment ==
=== MAFFT ===
+The following example uses the MAFFT program to align four sequences
+and then prints the result to the screen.
+Please note that if the path to the MAFFT executable is properly set `mafft=Bio::MAFFT.new(options)` can be used instead of explicitly indicating the path as in the example.
+
{{{
#!/usr/bin/env ruby
require 'bio'
-# Calculates the alignment using the MAFFT program
-# on the local machine, and stores the result in 'report'.
-options = [ '--maxiterate', '1000', '--localpair' ]
-mafft = Bio::MAFFT.new('path/to/mafft', options )
-report = mafft.query_align( seqs)
+# 'seqs' is either an array of sequences or a multiple sequence
+# alignment. In general this is read in from a file as described in ?.
+# For the purpose of this tutorial, it is generated in code.
+seqs = ["KMLFGVVFFFGG",
+ "LMGGHHF",
+ "GKKKKGHHHGHRRRGR",
+ "KKKKGHHHGHRRRGR"]
+
+
+# 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)
-# Accesses the actual alignment
+# 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 ===
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# 'seqs' is either an array of sequences or a multiple sequence
+# alignment. In general this is read in from a file as described in ?.
+# For the purpose of this tutorial, it is generated in code.
+seqs = ["KMLFGVVFFFGG",
+ "LMGGHHF",
+ "GKKKKGHHHGHRRRGR",
+ "KKKKGHHHGHRRRGR"]
+
+# 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.
+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
+
+=== 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 ==
+
+Oftentimes, multiple sequence to be used for phylogenetic inference are 'cleaned up' in some manner. For instance, some researchers prefer to delete columns with more than 50% gaps. The following code is an example of how to do that in !BioRuby.
+
+
+_... 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
+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'
+
+}}}
+
+
+=== PhyML ===
+
+_... 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..._
+
+
+== Others? ==
+
+
+----
+
+= Putting It All Together =
-Add your content here. Format your content with:
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\ No newline at end of file
+Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.
+
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff