X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=9972a5160a83817098f72ed1a02536e9ebcc9a6c;hb=dc7b38fb200e01f848623762f52bf345b51dad1d;hp=e3da58e093a25fcdd992ef6393dd10eb0a3309b0;hpb=0e9ba580fb2b0d19fc6f116cee31575baa6f19b2;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index e3da58e..9972a51 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -1,12 +1,16 @@
 #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 ===
@@ -19,6 +23,7 @@ require 'bio'
 
 }}}
 
+ 
 
 === Writing a Multiple Sequence Alignment to a File ===
 
@@ -32,10 +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.
 
 
@@ -50,21 +55,21 @@ require 'bio'
 # 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 
 
 
 
@@ -79,19 +84,24 @@ require 'bio'
 # 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 ==
 
@@ -108,6 +118,8 @@ require 'bio'
 }}}
 
 
+----
+
 = Phylogenetic Trees =
 
 == Phylogenetic Tree Input and Output ==
@@ -124,6 +136,8 @@ require 'bio'
 
 Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
 
+
+
 === Writing of Phylogenetic Trees ===
 
 _... to be done_
@@ -137,9 +151,14 @@ 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 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 ==
 
@@ -154,6 +173,7 @@ require 'bio'
 }}}
 
 
+
 == Pairwise Distance Based Methods ==
 
 === FastME ===
@@ -167,8 +187,23 @@ require 'bio'
 }}}
 
 
+
+=== PHYLIP? ===
+
+
+
+== Support Calculation? ==
+
+=== Bootstrap Resampling? ===
+
+
+----
+
 = Analyzing Phylogenetic Trees =
 
+== PAML ==
+
+
 == Gene Duplication Inference ==
 
 _need to further test and then import GSoC 'SDI' work..._