comparison hyphy_busted.xml @ 6:f9a193154a55 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author iuc
date Thu, 20 Feb 2020 18:16:58 -0500
parents d6389faa75ff
children cde38657e82c
comparison
equal deleted inserted replaced
5:8c8640ca39d7 6:f9a193154a55
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 BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection. 36
37 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
38 ===============================================================
39
40 What question does this method answer?
41 --------------------------------------
37 42
38 See the online documentation_ for more information. 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)?
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.),
47 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
39 48
40 .. _documentation: http://hyphy.org/methods/selection-methods/#busted 49 Recommended Applications
41 ]]></help> 50 ------------------------
51
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.
54
55 Brief description
56 -----------------
57
58 BUSTED (branch-site unrestricted statistical test of episodic
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
61 evidence of episodic diversifying selection. Assuming there is evidence
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
64 individual sites may have been subject to selection.
65
66
67 Input
68 -----
69
70 1. A *FASTA* sequence alignment.
71 2. A phylogenetic tree in the *Newick* format
72
73 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
74
75
76 Output
77 ------
78
79 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
80
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.
83
84 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
85
86 Further reading
87 ---------------
88
89 http://hyphy.org/methods/selection-methods/#busted
90
91
92 Tool options
93 ------------
94 ::
95
96
97 --code Which genetic code to use
98
99 --branches Which branches should be tested for selection?
100 All [default] : test all branches
101
102 Internal : test only internal branches (suitable for
103 intra-host pathogen evolution for example, where terminal branches
104 may contain polymorphism data)
105
106 Leaves: test only terminal (leaf) branches
107
108 Unlabeled: if the Newick string is labeled using the {} notation,
109 test only branches without explicit labels
110 (see http://hyphy.org/tutorials/phylotree/)
111 ]]>
112 </help>
42 <expand macro="citations"> 113 <expand macro="citations">
43 <citation type="doi">10.1093/molbev/msv035</citation> 114 <citation type="doi">10.1093/molbev/msv035</citation>
44 </expand> 115 </expand>
45 </tool> 116 </tool>