Mercurial > repos > iuc > hyphy_fel
diff hyphy_fel.xml @ 6:4eba0baf0278 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author | iuc |
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date | Thu, 20 Feb 2020 18:15:14 -0500 |
parents | 1b62167f7ab2 |
children | 8389039f7fbc |
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--- a/hyphy_fel.xml Mon Feb 17 14:54:30 2020 -0500 +++ b/hyphy_fel.xml Thu Feb 20 18:15:14 2020 -0500 @@ -23,7 +23,7 @@ <expand macro="gencode"/> <expand macro="branches"/> <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> - <param name="include_srv" type="select" label="Include synonymous rate variation"> + <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> @@ -40,12 +40,89 @@ </test> </tests> <help><![CDATA[ -FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny. +FEL : Fixed effects likelihood +============================== + +What question does this method answer? +-------------------------------------- + +Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? + +Recommended Applications +------------------------ + +The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics +(or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which +represent candidate sites subject to strong selective pressures across the entire phylogeny. + +FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. + +Brief description +----------------- + +FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) +and non-synonymous rates (beta), and uses a likelihood ratio test to +determine if beta != alpha at a site. The estimates aggregate +information over all branches, so the signal is derived from pervasive +diversification or conservation. A subset of branches can be selected +for testing as well, in which case an additional (nuisance) parameter +will be inferred -- the non-synonymous rate on branches NOT selected for +testing. + + +Input +----- + +1. A *FASTA* sequence alignment. +2. A phylogenetic tree in the *Newick* format + +Note: the names of sequences in the alignment must match the names of the sequences in the tree. + + +Output +------ -See the online documentation_ for more information. +A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). +A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example) + +Further reading +--------------- + +http://hyphy.org/methods/selection-methods/#FEL + + +Tool options +------------ + +:: + + --code Which genetic code to use -.. _documentation: http://hyphy.org/methods/selection-methods/#fel - ]]></help> + --branches Which branches should be tested for selection? + All [default] : test all branches + + Internal : test only internal branches (suitable for + intra-host pathogen evolution for example, where terminal branches + may contain polymorphism data) + + Leaves: test only terminal (leaf) branches + + Unlabeled: if the Newick string is labeled using the {} notation, + test only branches without explicit labels + (see http://hyphy.org/tutorials/phylotree/) + + --pvalue The significance level used to determine significance + + --srv Include site-to-site synonymous rate variation? + Yes [default] or No + + + + +]]> + + </help> + <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand>