From: cmzmasek@gmail.com Date: Thu, 24 Feb 2011 09:11:48 +0000 (+0000) Subject: Edited wiki page PhyloBioRuby through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fe6161f9ff04df6aad319a34d0d5d3d312cf77e5;p=jalview.git Edited wiki page PhyloBioRuby through web user interface. --- diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index bebd29b..f44e59b 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -32,10 +32,10 @@ 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. @@ -139,7 +139,9 @@ Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_do == 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 == @@ -166,9 +168,18 @@ require 'bio' }}} +=== PHYLIP? === + + +== Support Calculation? == + +=== Bootstrap Resampling? === + = Analyzing Phylogenetic Trees = +== PAML == + == Gene Duplication Inference == _need to further test and then import GSoC 'SDI' work..._