Edited wiki page PhyloBioRuby through web user interface.

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
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--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -1,15 +1,21 @@
 #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 =
 
-== Reading in Multiple Sequence Alignments from Files ==
 
-... to be done
+== Multiple Sequence Alignment Input and Output ==
+
+=== Reading in a Multiple Sequence Alignment from a File ===
+
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -17,10 +23,11 @@ require 'bio'
 
 }}}
 
+ 
 
-== Writing Multiple Sequence Alignments to Files ==
+=== Writing a Multiple Sequence Alignment to a File ===
 
-... to be done
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -30,10 +37,10 @@ require 'bio'
 
 
 
-== 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.
 
 
@@ -46,18 +53,25 @@ require 'bio'
 # 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 ===
 
@@ -68,26 +82,34 @@ 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)
+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 Alignments  ==
+ * 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 ==
 
 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
@@ -96,11 +118,29 @@ require 'bio'
 }}}
 
 
+----
+
 = Phylogenetic Trees =
 
-== Reading and Writing of 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
+
+
 
-*... to be done*
+=== Writing of Phylogenetic Trees ===
+
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -111,15 +151,20 @@ require 'bio'
 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
 
 
+
 == 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 ==
 
 === RAxML ===
 
-*... to be done*
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -128,11 +173,12 @@ require 'bio'
 }}}
 
 
+
 == Pairwise Distance Based Methods ==
 
 === FastME ===
 
-... to be done
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -141,11 +187,26 @@ require 'bio'
 }}}
 
 
+
+=== PHYLIP? ===
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
 = Analyzing Phylogenetic Trees =
 
+== PAML ==
+
+
 == Gene Duplication Inference ==
 
-*Need to further test and then import GSoC 'SDI' work.*
+_need to further test and then import GSoC 'SDI' work..._
 
 
-== Others? ==
+== Others? ==
\ No newline at end of file