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comparison hyphy_busted.xml @ 9:cb5ff3a1d7c6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
author iuc
date Wed, 22 Apr 2020 16:06:07 +0000
parents 51548f9a253f
children 4f0942146044
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8:ed1ec8d498ac 9:cb5ff3a1d7c6
31 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> 31 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
32 <output name="busted_output" file="busted-out1.json" compare="sim_size"/> 32 <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <help><![CDATA[ 35 <help><![CDATA[
36 36
37 BUSTED : Bayesian UnresTricted Test of Episodic Diversification 37 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
38 =============================================================== 38 ===============================================================
39 39
40 What question does this method answer? 40 What question does this method answer?
41 -------------------------------------- 41 --------------------------------------
42 42
43 Is there evidence that some sites in the alignment have been subject to positive diversifying selection, 43 Is there evidence that some sites in the alignment have been subject to positive diversifying selection,
44 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? 44 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
45 In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. 45 In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time.
46 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), 46 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
47 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power. 47 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
48 48
49 Recommended Applications 49 Recommended Applications
50 ------------------------ 50 ------------------------
51 51
52 1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? 52 1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)?
53 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. 53 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.
54 54
55 Brief description 55 Brief description
56 ----------------- 56 -----------------
57 57
59 diversification) uses a random effects branch-site model fitted jointly 59 diversification) uses a random effects branch-site model fitted jointly
60 to all or a subset of tree branches in order to test for alignment-wide 60 to all or a subset of tree branches in order to test for alignment-wide
61 evidence of episodic diversifying selection. Assuming there is evidence 61 evidence of episodic diversifying selection. Assuming there is evidence
62 of positive selection (i.e. there is an omega > 1), BUSTED will also 62 of positive selection (i.e. there is an omega > 1), BUSTED will also
63 perform a quick evidence-ratio style analysis to explore which 63 perform a quick evidence-ratio style analysis to explore which
64 individual sites may have been subject to selection. 64 individual sites may have been subject to selection.
65 65
66 66
67 Input 67 Input
68 ----- 68 -----
69 69
76 Output 76 Output
77 ------ 77 ------
78 78
79 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). 79 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
80 80
81 For each tested branch the analysis will infer the appropriate number of selective regimes, 81 For each tested branch the analysis will infer the appropriate number of selective regimes,
82 and whether or not there is statistical evidence of positive selection on that branch. 82 and whether or not there is statistical evidence of positive selection on that branch.
83 83
84 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example) 84 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
85 85
86 Further reading 86 Further reading
92 Tool options 92 Tool options
93 ------------ 93 ------------
94 :: 94 ::
95 95
96 96
97 --code Which genetic code to use 97 --code Which genetic code to use
98 98
99 --branches Which branches should be tested for selection? 99 --branches Which branches should be tested for selection?
100 All [default] : test all branches 100 All [default] : test all branches
101 101
102 Internal : test only internal branches (suitable for 102 Internal : test only internal branches (suitable for
103 intra-host pathogen evolution for example, where terminal branches 103 intra-host pathogen evolution for example, where terminal branches
104 may contain polymorphism data) 104 may contain polymorphism data)
105 105
106 Leaves: test only terminal (leaf) branches 106 Leaves: test only terminal (leaf) branches
107 107
108 Unlabeled: if the Newick string is labeled using the {} notation, 108 Unlabeled: if the Newick string is labeled using the {} notation,
109 test only branches without explicit labels 109 test only branches without explicit labels
110 (see http://hyphy.org/tutorials/phylotree/) 110 (see http://hyphy.org/tutorials/phylotree/)
111 ]]> 111 ]]>
112 </help> 112 </help>
113 <expand macro="citations"> 113 <expand macro="citations">
114 <citation type="doi">10.1093/molbev/msv035</citation> 114 <citation type="doi">10.1093/molbev/msv035</citation>