From 1833c6040979f79d80e28bf9de13f0bee1f0f8bb Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 15:51:38 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 41aa639..e45ddf6 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -50,6 +50,15 @@ In the following, examples for using the MAFFT and Muscle are shown. #!/usr/bin/env ruby require 'bio' +# 'seqs' is either an array of sequences or a multiple sequence +# alignment. In general this is read in from a file as described in ?. +# For the purpose of this tutorial, it is generated in code. +seqs = ["KMLFGVVFFFGG", + "LMGGHHF", + "GKKKKGHHHGHRRRGR", + "KKKKGHHHGHRRRGR"] + + # Calculates the alignment using the MAFFT program on the local # machine with options '--maxiterate 1000 --localpair' # and stores the result in 'report'. @@ -79,6 +88,14 @@ References: #!/usr/bin/env ruby require 'bio' +# 'seqs' is either an array of sequences or a multiple sequence +# alignment. In general this is read in from a file as described in ?. +# For the purpose of this tutorial, it is generated in code. +seqs = ["KMLFGVVFFFGG", + "LMGGHHF", + "GKKKKGHHHGHRRRGR", + "KKKKGHHHGHRRRGR"] + # Calculates the alignment using the Muscle program on the local # machine with options '-quiet -maxiters 64' # and stores the result in 'report'. @@ -100,13 +117,12 @@ References: === 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. +[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 == -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: +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. _... to be done_ -- 1.7.10.2