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comparison hyphy_meme.xml @ 5:4d5768ad6316 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author iuc
date Thu, 20 Feb 2020 18:11:41 -0500
parents 33040ebb30c6
children 74b590fdc6a0
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4:8366d5b28b49 5:4d5768ad6316
35 <param name="p_value" value="0.1"/> 35 <param name="p_value" value="0.1"/>
36 <output name="meme_output" file="meme-out1.json" compare="sim_size"/> 36 <output name="meme_output" file="meme-out1.json" compare="sim_size"/>
37 </test> 37 </test>
38 </tests> 38 </tests>
39 <help><![CDATA[ 39 <help><![CDATA[
40 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. 40 MEME: Mixed Effects Model of Evolution
41 ======================================
42
43 What question does this method answer?
44 --------------------------------------
41 45
42 See the online documentation_ for more information. 46 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
47 single lineage or subset of lineages, diversifying selection?
43 48
44 .. _documentation: http://hyphy.org/methods/selection-methods/#meme 49 Recommended Applications
50 ------------------------
51
52 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
53 (or balancing selection), including adaptive immune escape by viruses.
54 MEME is ideally suited to identify sites under positive selection which
55 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
56
57 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
58 MEME is therefore our recommended method if maximum power is desired.
59
60
61 Brief description
62 -----------------
63
64 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous
65 (alpha) and a two-category mixture of non-synonymous (beta-, with
66 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a
67 likelihood ratio test to determine if beta+ > &alpha; at a site. The
68 estimates aggregate information over a proportion of branches at a site,
69 so the signal is derived from episodic diversification, which is a
70 combination of strength of selection [effect size] and the proportion of
71 the tree affected. A subset of branches can be selected for testing as
72 well, in which case an additional (nuisance) parameter will be inferred
73 -- the non-synonymous rate on branches NOT selected for testing.
74
75 Input
76 -----
77
78 1. A *FASTA* sequence alignment.
79 2. A phylogenetic tree in the *Newick* format
80
81 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
82
83
84 Output
85 ------
86
87 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
88
89 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example)
90
91 Further reading
92 ---------------
93
94 http://hyphy.org/methods/selection-methods/#MEME
95
96
97 Tool options
98 ------------
99 ::
100
101
102 --code Which genetic code to use
103
104 --branches Which branches should be tested for selection?
105 All [default] : test all branches
106
107 Internal : test only internal branches (suitable for
108 intra-host pathogen evolution for example, where terminal branches
109 may contain polymorphism data)
110
111 Leaves: test only terminal (leaf) branches
112
113 Unlabeled: if the Newick string is labeled using the {} notation,
114 test only branches without explicit labels
115 (see http://hyphy.org/tutorials/phylotree/)
116
117 --pvalue The significance level used to determine significance
118
119
45 ]]></help> 120 ]]></help>
46 <expand macro="citations"> 121 <expand macro="citations">
47 <citation type="doi">10.1371/journal.pgen.1002764</citation> 122 <citation type="doi">10.1371/journal.pgen.1002764</citation>
48 </expand> 123 </expand>
49 </tool> 124 </tool>