From 5425e0de2c8c9b05372014509c43cbde445f2319 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 1 Mar 2011 03:42:49 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 3839645..70ed776 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -165,9 +165,12 @@ References: === Other Programs === +_need more detail here..._ + [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 == Oftentimes, multiple sequence to be used for phylogenetic inference are 'cleaned up' in some manner. For instance, some researchers prefer to delete columns with more than 50% gaps. The following code is an example of how to do that in !BioRuby. @@ -192,13 +195,25 @@ require 'bio' _... to be done_ +====Newick or New Hamphshire Format==== + {{{ #!/usr/bin/env ruby require 'bio' }}} -Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation +====phyloXML Format==== + +Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation]. + +{{{ +#!/usr/bin/env ruby +require 'bio' + +}}} + +Also, see: -- 1.7.10.2