From 799553f205ee4467356d37225bc666951cb74ca9 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 09:13:45 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index f44e59b..ac84843 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -1,12 +1,16 @@ #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development! + + = Introduction = Tutorial for multiple sequence alignments and phylogenetic methods in !BioRuby -- under development! + = Multiple Sequence Alignments = + == Multiple Sequence Alignment Input and Output == === Reading in a Multiple Sequence Alignment from a File === @@ -19,6 +23,7 @@ require 'bio' }}} + === Writing a Multiple Sequence Alignment to a File === @@ -93,6 +98,8 @@ References: * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797 + + == Manipulating Multiple Sequence Alignments == It is probably a good idea to 'clean up' multiple sequence to be used @@ -108,6 +115,7 @@ require 'bio' }}} + = Phylogenetic Trees = == Phylogenetic Tree Input and Output == @@ -124,6 +132,8 @@ require 'bio' Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation + + === Writing of Phylogenetic Trees === _... to be done_ @@ -137,12 +147,15 @@ require 'bio' Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation + == 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 FastME..._ _What about pairwise distance calculation?_ + + == Maximum Likelihood == === RAxML === @@ -156,6 +169,7 @@ require 'bio' }}} + == Pairwise Distance Based Methods == === FastME === @@ -168,21 +182,27 @@ require 'bio' }}} + + === PHYLIP? === + == Support Calculation? == === Bootstrap Resampling? === + = Analyzing Phylogenetic Trees = == PAML == + == Gene Duplication Inference == _need to further test and then import GSoC 'SDI' work..._ -== Others? == \ No newline at end of file +== Others? == + -- 1.7.10.2