Mercurial > repos > iuc > hyphy_busted
changeset 10:cde38657e82c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
| author | iuc |
|---|---|
| date | Wed, 22 Apr 2020 12:13:37 -0400 |
| parents | 6647e04e92a7 |
| children | 7bed09107277 |
| files | hyphy_busted.xml macros.xml |
| diffstat | 2 files changed, 16 insertions(+), 16 deletions(-) [+] |
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--- a/hyphy_busted.xml Fri Mar 27 12:30:54 2020 -0400 +++ b/hyphy_busted.xml Wed Apr 22 12:13:37 2020 -0400 @@ -33,23 +33,23 @@ </test> </tests> <help><![CDATA[ - + BUSTED : Bayesian UnresTricted Test of Episodic Diversification -=============================================================== - +=============================================================== + What question does this method answer? -------------------------------------- -Is there evidence that some sites in the alignment have been subject to positive diversifying selection, -either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? -In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. +Is there evidence that some sites in the alignment have been subject to positive diversifying selection, +either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? +In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power. Recommended Applications ------------------------ -1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? +1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? 2. Testing small or low-divergence alignments (i.e. ~30 sequences) for evidence of positive diversifying selection, where neither branch nor site level methods have sufficient power. Brief description @@ -61,7 +61,7 @@ evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which -individual sites may have been subject to selection. +individual sites may have been subject to selection. Input @@ -78,7 +78,7 @@ A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). -For each tested branch the analysis will infer the appropriate number of selective regimes, +For each tested branch the analysis will infer the appropriate number of selective regimes, and whether or not there is statistical evidence of positive selection on that branch. A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example) @@ -94,19 +94,19 @@ :: - --code Which genetic code to use + --code Which genetic code to use --branches Which branches should be tested for selection? All [default] : test all branches - - Internal : test only internal branches (suitable for + + 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 + test only branches without explicit labels (see http://hyphy.org/tutorials/phylotree/) ]]> </help>
--- a/macros.xml Fri Mar 27 12:30:54 2020 -0400 +++ b/macros.xml Wed Apr 22 12:13:37 2020 -0400 @@ -106,7 +106,7 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.8</token> + <token name="@VERSION@">2.5.9</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement>