From 7f6a904694d29b48334c4dc6fcc25c9f76966cc5 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 08:29:47 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index b6fecdf..c5f1cb3 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -2,7 +2,7 @@ = 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 = @@ -20,7 +20,7 @@ require 'bio' == Calculating a Multiple Sequence Alignment == -BioRuby! can be used to execute a variety of multiple sequence alignment +!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. @@ -84,13 +84,30 @@ require 'bio' }}} -= Phylogenetic Inference = += Phylogenetic Trees = + +== Reading and 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 any wrappers for phylogenetic inference, I am progress of writing a RAxML wrapper followed by a wrapper for FastMA.* == Maximum Likelihood == === RAxML === -... to be done +*... to be done* {{{ #!/usr/bin/env ruby @@ -110,3 +127,4 @@ require 'bio' require 'bio' }}} + -- 1.7.10.2