Mercurial > repos > iuc > hyphy_meme
annotate hyphy_meme.xml @ 30:45a2366d777e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9ef881c2d3d5f240cbff33667b55f72cb82d9896"
author | iuc |
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date | Tue, 05 Oct 2021 05:04:06 +0000 |
parents | e0763df98352 |
children | cdbb233119cb |
rev | line source |
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7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 <?xml version="1.0"?> |
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e0763df98352
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy2" profile="19.09"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>Mixed Effects Model of Evolution</description> |
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45a2366d777e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9ef881c2d3d5f240cbff33667b55f72cb82d9896"
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4 <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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5 <macros> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 <import>macros.xml</import> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 </macros> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 <expand macro="requirements"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 <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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10 @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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11 @HYPHYMPI@ meme |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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12 --alignment ./$input_file |
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e0763df98352
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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13 @INPUT_TREE@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --code '$gencodeid' |
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e0763df98352
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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15 @branch_options@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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16 --pvalue '$p_value' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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17 --output '$meme_output' |
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2f07f5b4e47b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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18 --full-model '$full_model' |
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e0763df98352
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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19 @ERRORS@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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20 ]]></command> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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21 <inputs> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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22 <expand macro="inputs"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 <expand macro="gencode"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 <expand macro="branches"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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26 <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 </inputs> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 <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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29 <data name="meme_output" format="hyphy_results.json" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 </outputs> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 <param name="input_file" ftype="fasta" value="meme-in1.fa"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 <param name="branches" value="All"/> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 <param name="p_value" value="0.1"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 795426da748ca2c21d52b72b2a78e8e6135e4079"
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37 <output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 </test> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 </tests> |
7b3f9c78cf6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 <help><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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41 MEME: Mixed Effects Model of Evolution |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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42 ====================================== |
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43 |
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44 What question does this method answer? |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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45 -------------------------------------- |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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46 |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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47 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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48 single lineage or subset of lineages, diversifying selection? |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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49 |
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50 Recommended Applications |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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51 ------------------------ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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52 |
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53 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics |
3d1f153e2aa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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54 (or balancing selection), including adaptive immune escape by viruses. |
3d1f153e2aa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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55 MEME is ideally suited to identify sites under positive selection which |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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56 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny. |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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57 |
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58 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. |
3d1f153e2aa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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59 MEME is therefore our recommended method if maximum power is desired. |
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60 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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61 |
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62 Brief description |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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63 ----------------- |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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64 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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65 MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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66 (alpha) and a two-category mixture of non-synonymous (beta-, with |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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67 proportion p-, and beta+ with proportion [1-p-]) rates, and uses a |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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68 likelihood ratio test to determine if beta+ > α at a site. The |
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69 estimates aggregate information over a proportion of branches at a site, |
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70 so the signal is derived from episodic diversification, which is a |
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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 combination of strength of selection [effect size] and the proportion of |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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72 the tree affected. A subset of branches can be selected for testing as |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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73 well, in which case an additional (nuisance) parameter will be inferred |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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74 -- the non-synonymous rate on branches NOT selected for testing. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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75 |
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76 Input |
4d5768ad6316
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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77 ----- |
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78 |
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79 1. A *FASTA* sequence alignment. |
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80 2. A phylogenetic tree in the *Newick* format |
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81 |
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82 Note: the names of sequences in the alignment must match the names of the sequences in the tree. |
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83 |
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84 |
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85 Output |
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86 ------ |
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87 |
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88 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). |
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89 |
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90 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example) |
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91 |
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92 Further reading |
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93 --------------- |
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94 |
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95 http://hyphy.org/methods/selection-methods/#MEME |
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96 |
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97 |
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98 Tool options |
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99 ------------ |
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100 :: |
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101 |
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102 |
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103 --code Which genetic code to use |
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104 |
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105 --branches Which branches should be tested for selection? |
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106 All [default] : test all branches |
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107 |
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108 Internal : test only internal branches (suitable for |
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109 intra-host pathogen evolution for example, where terminal branches |
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110 may contain polymorphism data) |
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111 |
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112 Leaves: test only terminal (leaf) branches |
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113 |
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114 Unlabeled: if the Newick string is labeled using the {} notation, |
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115 test only branches without explicit labels |
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116 (see http://hyphy.org/tutorials/phylotree/) |
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117 |
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118 --pvalue The significance level used to determine significance |
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119 |
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120 |
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121 ]]></help> |
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122 <expand macro="citations"> |
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123 <citation type="doi">10.1371/journal.pgen.1002764</citation> |
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124 </expand> |
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125 </tool> |