Mercurial > repos > iuc > hyphy_busted
annotate hyphy_busted.xml @ 35:e908c4003bd8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author | iuc |
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date | Thu, 02 Mar 2023 15:18:01 +0000 |
parents | e931e69b5a80 |
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35
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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2 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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3 <macros> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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4 <import>macros.xml</import> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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5 </macros> |
33
e931e69b5a80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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6 <expand macro="bio_tools"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 <expand macro="requirements"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9 @SYMLINK_FILES@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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10 hyphy busted |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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11 --alignment ./$input_file |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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12 @INPUT_TREE@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --code $gencodeid |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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14 @branch_options@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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15 --output '$busted_output' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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16 @advanced_options@ |
70fab57f3c05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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17 @ERRORS@ |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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18 ]]></command> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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19 <inputs> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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20 <expand macro="inputs"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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21 <expand macro="gencode"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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22 <expand macro="branches"/> |
26
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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23 <expand macro="srv"/> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
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24 </inputs> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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25 <outputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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26 <data name="busted_output" format="hyphy_results.json" /> |
26
70fab57f3c05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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27 <expand macro="alternative_model_output" /> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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28 </outputs> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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29 <tests> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
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30 <test> |
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b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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32 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
35
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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33 <output name="busted_output"> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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34 <assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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35 <has_size value="113683" delta="2000"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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36 <has_text text="substitutions"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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37 <has_text text="test results"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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38 </assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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39 </output> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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40 </test> |
26
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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41 <test> |
70fab57f3c05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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42 <param name="input_file" ftype="nex" value="busted-in2.nex"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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43 <conditional name="branch_cond"> |
d09dd951d0c4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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44 <param name="branch_sel" value="specify"/> |
d09dd951d0c4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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45 <param name="branch_label" value="B_US_90_WEAU160_BRANCH" /> |
d09dd951d0c4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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46 </conditional> |
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47 <param name="srv_options" value="specify" /> |
70fab57f3c05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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48 <param name="save_alternative_model" value="true" /> |
35
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49 <output name="busted_output"> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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50 <assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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51 <has_size value="112119" delta="2000"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
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52 <has_text text="substitutions"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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53 <has_text text="test results"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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54 </assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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55 </output> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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56 <output name="alternative_model"> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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57 <assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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58 <has_size value="333928" delta="2000"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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59 <has_text text="END;"/> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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60 </assert_contents> |
e908c4003bd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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61 </output> |
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62 </test> |
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63 </tests> |
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64 <help><![CDATA[ |
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65 |
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66 BUSTED : Bayesian UnresTricted Test of Episodic Diversification |
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67 =============================================================== |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
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68 |
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69 What question does this method answer? |
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70 -------------------------------------- |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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71 |
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72 Is there evidence that some sites in the alignment have been subject to positive diversifying selection, |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
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73 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
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74 In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. |
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75 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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76 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power. |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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77 |
f9a193154a55
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78 Recommended Applications |
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79 ------------------------ |
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80 |
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81 1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? |
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82 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. |
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83 |
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84 Brief description |
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85 ----------------- |
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86 |
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87 BUSTED (branch-site unrestricted statistical test of episodic |
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88 diversification) uses a random effects branch-site model fitted jointly |
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89 to all or a subset of tree branches in order to test for alignment-wide |
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90 evidence of episodic diversifying selection. Assuming there is evidence |
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91 of positive selection (i.e. there is an omega > 1), BUSTED will also |
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92 perform a quick evidence-ratio style analysis to explore which |
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93 individual sites may have been subject to selection. |
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94 |
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95 |
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96 Input |
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97 ----- |
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98 |
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99 1. A *FASTA* sequence alignment. |
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100 2. A phylogenetic tree in the *Newick* format |
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101 |
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102 Note: the names of sequences in the alignment must match the names of the sequences in the tree. |
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103 |
6
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104 |
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105 Output |
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106 ------ |
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107 |
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108 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). |
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109 |
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110 For each tested branch the analysis will infer the appropriate number of selective regimes, |
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111 and whether or not there is statistical evidence of positive selection on that branch. |
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112 |
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113 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example) |
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114 |
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115 Further reading |
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116 --------------- |
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117 |
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118 http://hyphy.org/methods/selection-methods/#busted |
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119 |
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120 |
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121 Tool options |
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122 ------------ |
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123 :: |
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124 |
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125 |
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126 --code Which genetic code to use |
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127 |
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128 --branches Which branches should be tested for selection? |
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129 All [default] : test all branches |
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130 |
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131 Internal : test only internal branches (suitable for |
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132 intra-host pathogen evolution for example, where terminal branches |
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133 may contain polymorphism data) |
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134 |
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135 Leaves: test only terminal (leaf) branches |
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136 |
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137 Unlabeled: if the Newick string is labeled using the {} notation, |
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138 test only branches without explicit labels |
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139 (see http://hyphy.org/tutorials/phylotree/) |
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140 ]]> |
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141 </help> |
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142 <expand macro="citations"> |
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143 <citation type="doi">10.1093/molbev/msv035</citation> |
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144 </expand> |
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145 </tool> |