From ff39f35fbb20f2610af44c2b7bc45d29f4bfa80b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 08:35:37 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 31 ++++++++++++++++++++++++++----- 1 file changed, 26 insertions(+), 5 deletions(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index c5f1cb3..45c0d5f 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -7,7 +7,7 @@ Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby - = Multiple Sequence Alignments = -== Reading in a Multiple Sequence Alignment from a File == +== Reading in Multiple Sequence Alignments from Files == ... to be done @@ -18,15 +18,26 @@ require 'bio' }}} -== Calculating a Multiple Sequence Alignment == +== Writing Multiple Sequence Alignments to Files == + +... to be done + +{{{ +#!/usr/bin/env ruby +require 'bio' + +}}} + + + +== 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]). In the following, examples for using the MAFFT and Muscle are shown. -=== MAFFT === - +=== MAFFT === {{{ #!/usr/bin/env ruby @@ -47,6 +58,7 @@ report.align.each { |s| puts s.to_s } # }}} + === Muscle === {{{ @@ -69,7 +81,7 @@ report.align.each { |s| puts s.to_s } }}} -== Manipulating Multiple Sequence Alignment == +== 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: @@ -128,3 +140,12 @@ require 'bio' }}} + += Analyzing Phylogenetic Trees = + +== Gene Duplication Inference == + +*Need to further test and then import GSoC 'SDI' work.* + + +== Others? == -- 1.7.10.2