Mercurial > repos > iuc > hyphy_fubar

annotate hyphy_fubar.xml @ 36:da919379e8e4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:40:57 +0000
parents d44c0b7a6cb8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
d44c0b7a6cb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
1 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
2 <description>Fast Unconstrained Bayesian AppRoximation</description>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
3 <macros>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
5 </macros>
33
a0b0fef4062b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
6 <expand macro="bio_tools"/>
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
7 <expand macro="requirements"/>
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
24
0eb70c561b06 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
9 @SYMLINK_FILES@
26
c1e86d0fbb57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
10 ln -s '$fubar_output' ${input_file}.FUBAR.json &&
3
d92fc00e1e9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
11 hyphy fubar
24
0eb70c561b06 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
12 --alignment ./$input_file
26
c1e86d0fbb57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
13 @INPUT_TREE@
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
14 --code '$gencodeid'
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
15 --method '$posteriorEstimationMethod.method'
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
16 @posteriorEstimationMethod_cmd@
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
17 --grid '$advanced_options.grid_points'
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
18 --concentration_parameter '$advanced_options.concentration'
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
19 --non-zero $advanced_options.non_zero
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
20 --kill-zero-lengths $advanced_options.kill_zero_lengths
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
21 > fubar_stdout.md
26
c1e86d0fbb57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
22 @ERRORS@
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
23 ]]></command>
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
24 <inputs>
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
25 <expand macro="inputs"/>
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
26 <expand macro="gencode"/>
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
27 <expand macro="conditional_posteriorEstimationMethod" />
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
28 <section name="advanced_options" title="Advanced Options" expanded="false">
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
29 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" help="The number of grid points used to approximate the posterior distribution of dN and dS." />
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
30 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" help="The concentration parameter of the Dirichlet prior on the grid weights." />
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
31 <param argument="--non-zero" type="boolean" truevalue="Yes" falsevalue="No" label="Enforce non-zero synonymous rates" help="Enforce non-zero synonymous rates on the grid. This is useful for calculating dN/dS ratios, as it prevents division by zero."/>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
32 <expand macro="kill_zero_lengths_param"/>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
33 </section>
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
34
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
35 </inputs>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
36 <outputs>
24
0eb70c561b06 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
37 <data name="fubar_output" format="hyphy_results.json" />
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
38 <data name="fubar_md_report" format="markdown" from_work_dir="fubar_stdout.md" label="FUBAR Report (Markdown) for ${tool.name} on ${on_string}" />
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
39 </outputs>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
40 <tests>
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
41 <test expect_num_outputs="2">
24
0eb70c561b06 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
42 <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
43 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>
32
cf9bd1a41ba5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 31
diff changeset
44 <conditional name="posteriorEstimationMethod">
cf9bd1a41ba5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 31
diff changeset
45 <param name="method" value="Variational-Bayes"/>
cf9bd1a41ba5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 31
diff changeset
46 </conditional>
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
47 <output name="fubar_output">
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
48 <assert_contents>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
49 <has_text text="Empiricial Bayes Factor for positive selection at a site"/>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
50 </assert_contents>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
51 </output>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
52 <output name="fubar_md_report">
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
53 <assert_contents>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
54 <has_text text="Running an iterative zeroth order variational Bayes procedure to estimate the posterior mean of rate weights"/>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
55 <has_text text="### Tabulating site-level results"/>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
56 </assert_contents>
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
57 </output>
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
58 </test>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
59 </tests>
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
60 <help><![CDATA[
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
61
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
62 FUBAR : Faste Unbiased Bayesian AppRoximation
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
63 =============================================
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
64
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
65 What question does this method answer?
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
66 --------------------------------------
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
67
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
68 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
69
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
70 Recommended Applications
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
71 ------------------------
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
72
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
73 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
74 (or balancing selection), including adaptive immune escape by viruses. As such, FUBAR is ideally suited to identify sites under positive selection which
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
75 represent candidate sites subject to strong selective pressures across the entire phylogeny.
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
76
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
77 FUBAR is our recommended method for detecting pervasive selection at individual sites on large (> 500 sequences) datasets for which other methods have prohibitive runtimes, unless you have access to a computer cluster.
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
78
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
79 Brief description
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
80 -----------------
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
81
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
82 FUBAR (Fast, Unconstrained Bayesian AppRoximation) is a Bayesian method for detecting site-specific positive and negative selection. It is designed to be fast and efficient, making it suitable for large datasets.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
83
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
84 The core idea behind FUBAR is to model the non-synonymous (dN) and synonymous (dS) substitution rates at each site in a codon alignment. The ratio of these rates (dN/dS, or omega) is a measure of the selective pressure acting on a site. An omega value greater than 1 indicates positive (diversifying) selection, a value less than 1 indicates negative (purifying) selection, and a value of 1 indicates neutral evolution.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
85
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
86 FUBAR uses a Bayesian approach to infer the posterior distribution of dN and dS at each site. It does this by discretizing the dN and dS rates into a grid of points and then using a Bayesian graphical model to infer the posterior probability of each grid point for each site. This approach is much faster than traditional MCMC-based methods, which require long run times to converge.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
87
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
88 FUBAR offers three different methods for estimating the posterior distribution:
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
89
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
90 * **Variational-Bayes:** A fast approximation method that is the recommended default.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
91 * **Collapsed-Gibbs:** A faster MCMC method.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
92 * **Metropolis-Hastings:** The original, slowest MCMC method.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
93
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
94 Input
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
95 -----
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
96
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
97 1. A *FASTA* sequence alignment.
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
98 2. A phylogenetic tree in the *Newick* format
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
99
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
100 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
101
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
102
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
103 Output
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
104 ------
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
105
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
106 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
2
0e02271cfc93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
107
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
108 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FUBAR for an example)
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
109
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
110 Further reading
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
111 ---------------
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
112
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
113 http://hyphy.org/methods/selection-methods/#FUBAR
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
114
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
115
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
116 Tool options
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
117 ------------
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
118 ::
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
119
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
120
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
121 --code Which genetic code to use
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
122
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
123 --grid The number of grid points used to approximate the posterior distribution of dN and dS. A larger grid will provide a more accurate approximation but will also be slower. The default value of 20 is a good compromise between speed and accuracy.
2
0e02271cfc93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
124
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
125 --method The inference method to use for estimating the posterior distribution.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
126 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default]
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
127 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest]
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
128 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed]
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
129
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
130
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
131 --chains The number of MCMC chains to run. This is only applicable to the Metropolis-Hastings and Collapsed-Gibbs methods. A larger number of chains will provide a better exploration of the posterior distribution but will also be slower.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
132 default value: 5
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
133
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
134 --chain-length The length of each MCMC chain. This is only applicable to the Metropolis-Hastings and Collapsed-Gibbs methods. A longer chain will provide a better exploration of the posterior distribution but will also be slower.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
135 default value: 2,000,000
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
136
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
137 --burn-in The number of samples to discard from the beginning of each MCMC chain. This is done to ensure that the chain has converged to the posterior distribution. This is only applicable to the Metropolis-Hastings and Collapsed-Gibbs methods.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
138 default value: 1,000,000
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
139
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
140 --samples The number of samples to draw from each MCMC chain after the burn-in period. These samples are used to estimate the posterior distribution. This is only applicable to the Metropolis-Hastings and Collapsed-Gibbs methods.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
141 default value: 1,000
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
142
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
143 --concentration_parameter
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
144 The concentration parameter of the Dirichlet prior on the grid weights.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
145 default value: 0.5
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
146
36
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
147 --non-zero Enforce non-zero synonymous rates on the grid. This is useful for calculating dN/dS ratios, as it prevents division by zero.
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
148
da919379e8e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
149 --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency. This will not affect the results.
6
23cc51272855 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
150
1
5bd05fa94ffc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
151 ]]></help>
0
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
152 <expand macro="citations">
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
153 <citation type="doi">10.1093/molbev/mst030</citation>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
154 </expand>
0943d89b7a25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
155 </tool>