Mercurial > repos > iuc > hyphy_fel
comparison 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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21 <inputs> | 21 <inputs> |
22 <expand macro="inputs"/> | 22 <expand macro="inputs"/> |
23 <expand macro="gencode"/> | 23 <expand macro="gencode"/> |
24 <expand macro="branches"/> | 24 <expand macro="branches"/> |
25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> | 25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> |
26 <param name="include_srv" type="select" label="Include synonymous rate variation"> | 26 <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> |
27 <option value="Yes">Yes (recommended)</option> | 27 <option value="Yes">Yes (recommended)</option> |
28 <option value="No">No</option> | 28 <option value="No">No</option> |
29 </param> | 29 </param> |
30 </inputs> | 30 </inputs> |
31 <outputs> | 31 <outputs> |
38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | 38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
39 <output name="fel_output" file="fel-out1.json" compare="sim_size"/> | 39 <output name="fel_output" file="fel-out1.json" compare="sim_size"/> |
40 </test> | 40 </test> |
41 </tests> | 41 </tests> |
42 <help><![CDATA[ | 42 <help><![CDATA[ |
43 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. | 43 FEL : Fixed effects likelihood |
44 ============================== | |
45 | |
46 What question does this method answer? | |
47 -------------------------------------- | |
44 | 48 |
45 See the online documentation_ for more information. | 49 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? |
46 | 50 |
47 .. _documentation: http://hyphy.org/methods/selection-methods/#fel | 51 Recommended Applications |
48 ]]></help> | 52 ------------------------ |
53 | |
54 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics | |
55 (or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which | |
56 represent candidate sites subject to strong selective pressures across the entire phylogeny. | |
57 | |
58 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. | |
59 | |
60 Brief description | |
61 ----------------- | |
62 | |
63 FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) | |
64 and non-synonymous rates (beta), and uses a likelihood ratio test to | |
65 determine if beta != alpha at a site. The estimates aggregate | |
66 information over all branches, so the signal is derived from pervasive | |
67 diversification or conservation. A subset of branches can be selected | |
68 for testing as well, in which case an additional (nuisance) parameter | |
69 will be inferred -- the non-synonymous rate on branches NOT selected for | |
70 testing. | |
71 | |
72 | |
73 Input | |
74 ----- | |
75 | |
76 1. A *FASTA* sequence alignment. | |
77 2. A phylogenetic tree in the *Newick* format | |
78 | |
79 Note: the names of sequences in the alignment must match the names of the sequences in the tree. | |
80 | |
81 | |
82 Output | |
83 ------ | |
84 | |
85 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). | |
86 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example) | |
87 | |
88 Further reading | |
89 --------------- | |
90 | |
91 http://hyphy.org/methods/selection-methods/#FEL | |
92 | |
93 | |
94 Tool options | |
95 ------------ | |
96 | |
97 :: | |
98 | |
99 --code Which genetic code to use | |
100 | |
101 --branches Which branches should be tested for selection? | |
102 All [default] : test all branches | |
103 | |
104 Internal : test only internal branches (suitable for | |
105 intra-host pathogen evolution for example, where terminal branches | |
106 may contain polymorphism data) | |
107 | |
108 Leaves: test only terminal (leaf) branches | |
109 | |
110 Unlabeled: if the Newick string is labeled using the {} notation, | |
111 test only branches without explicit labels | |
112 (see http://hyphy.org/tutorials/phylotree/) | |
113 | |
114 --pvalue The significance level used to determine significance | |
115 | |
116 --srv Include site-to-site synonymous rate variation? | |
117 Yes [default] or No | |
118 | |
119 | |
120 | |
121 | |
122 ]]> | |
123 | |
124 </help> | |
125 | |
49 <expand macro="citations"> | 126 <expand macro="citations"> |
50 <citation type="doi">10.1093/molbev/msi105</citation> | 127 <citation type="doi">10.1093/molbev/msi105</citation> |
51 </expand> | 128 </expand> |
52 </tool> | 129 </tool> |