diff hyphy_meme.xml @ 5:4d5768ad6316 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"

--- a/hyphy_meme.xml	Mon Feb 17 14:53:45 2020 -0500
+++ b/hyphy_meme.xml	Thu Feb 20 18:11:41 2020 -0500
@@ -37,11 +37,86 @@
         </test>
     </tests>
     <help><![CDATA[
-MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches.
+MEME: Mixed Effects Model of Evolution
+======================================
+    
+What question does this method answer?
+--------------------------------------
+
+Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
+single lineage or subset of lineages, 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. 
+MEME is ideally suited to identify sites under positive selection which 
+represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
+
+MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. 
+MEME is therefore our recommended method if maximum power is desired. 
+
+
+Brief description
+-----------------
+
+MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
+(alpha) and a two-category mixture of non-synonymous (beta-, with
+proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
+likelihood ratio test to determine if beta+ > &alpha; at a site. The
+estimates aggregate information over a proportion of branches at a site,
+so the signal is derived from episodic diversification, which is a
+combination of strength of selection [effect size] and the proportion of
+the tree affected. 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
+-----
 
-See the online documentation_ for more information.
+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
+------
+
+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/MEME for an example)
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#MEME
+
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#meme
+Tool options
+------------
+::
+
+
+    --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 
+                            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
+     
+
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1371/journal.pgen.1002764</citation>