Mercurial > repos > iuc > hyphy_absrel
comparison hyphy_absrel.xml @ 6:f73435dc282b 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 18:17:51 -0500 |
parents | 181f5b9f139f |
children | cce7b18495e4 |
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5:bf204aabbf56 | 6:f73435dc282b |
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37 <param name="log" value="false"/> | 37 <param name="log" value="false"/> |
38 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> | 38 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> |
39 </test> | 39 </test> |
40 </tests> | 40 </tests> |
41 <help><![CDATA[ | 41 <help><![CDATA[ |
42 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch. | 42 |
43 aBSREL : Adaptive Branch-Site Random Effects Likelihood | |
44 ======================================================= | |
45 | |
46 What question does this method answer? | |
47 -------------------------------------- | |
43 | 48 |
44 See the online documentation_ for more information. | 49 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny? |
45 | 50 |
46 .. _documentation: http://hyphy.org/methods/selection-methods/#absrel | 51 Recommended Applications |
52 ------------------------ | |
53 | |
54 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences). | |
55 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) | |
56 | |
57 Brief description | |
58 ----------------- | |
59 | |
60 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive | |
61 random effects branch-site model framework to test whether each branch | |
62 has evolved under positive selection, using a procedure which infers an | |
63 optimal number of rate categories per branch. | |
64 | |
65 | |
66 Input | |
67 ----- | |
68 | |
69 1. A *FASTA* sequence alignment. | |
70 2. A phylogenetic tree in the *Newick* format | |
71 | |
72 Note: the names of sequences in the alignment must match the names of the sequences in the tree. | |
73 | |
74 | |
75 Output | |
76 ------ | |
77 | |
78 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). | |
79 | |
80 For each tested branch the analysis will infer the appropriate number of selective regimes, | |
81 and whether or not there is statistical evidence of positive selection on that branch. | |
82 | |
83 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example) | |
84 | |
85 Further reading | |
86 --------------- | |
87 | |
88 http://hyphy.org/methods/selection-methods/#absrel | |
89 | |
90 | |
91 Tool options | |
92 ------------ | |
93 :: | |
94 | |
95 | |
96 --code Which genetic code to use | |
97 | |
98 --branches Which branches should be tested for selection? | |
99 All [default] : test all branches | |
100 | |
101 Internal : test only internal branches (suitable for | |
102 intra-host pathogen evolution for example, where terminal branches | |
103 may contain polymorphism data) | |
104 | |
105 Leaves: test only terminal (leaf) branches | |
106 | |
107 Unlabeled: if the Newick string is labeled using the {} notation, | |
108 test only branches without explicit labels | |
109 (see http://hyphy.org/tutorials/phylotree/) | |
110 | |
111 | |
112 | |
47 ]]></help> | 113 ]]></help> |
48 <expand macro="citations"> | 114 <expand macro="citations"> |
49 <citation type="doi">10.1093/molbev/msv022</citation> | 115 <citation type="doi">10.1093/molbev/msv022</citation> |
50 </expand> | 116 </expand> |
51 </tool> | 117 </tool> |