Mercurial > repos > iuc > hyphy_busted
comparison hyphy_busted.xml @ 10:cde38657e82c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
| author | iuc |
|---|---|
| date | Wed, 22 Apr 2020 12:13:37 -0400 |
| parents | f9a193154a55 |
| children | c92d5ec5d8d7 |
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| 9:6647e04e92a7 | 10:cde38657e82c |
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| 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> |