Mercurial > repos > iuc > hyphy_bgm

annotate hyphy_bgm.xml @ 10:cd9063b57f8b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e86817831c8ab0d0f8f86e32c25027cc370947c5"
author iuc
date Mon, 27 Apr 2020 13:12:35 -0400
parents 823a5afee916
children 26ad9a6b1293
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bf97cacc1a55 "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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1df765cc6bcb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6b2cd926797bb94fba9d0e319a2dbcff6ee37735"
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2 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>- Detecting coevolving sites via Bayesian graphical models</description>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 <macros>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 <import>macros.xml</import>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 </macros>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 <expand macro="requirements"/>
bf97cacc1a55 "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[
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 ln -s '$input_file' bgm_input.fa &&
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_nhx' bgm_input.nhx &&
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f2c6ada85b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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11 hyphy bgm
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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12 --alignment ./bgm_input.fa
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --tree ./bgm_input.nhx
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --run_type $datatype.value
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 #if $datatype.value == "codon":
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16 --code '$datatype.gencodeid'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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17 #end if
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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18 #if $datatype.value == "protein":
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19 --baseline_model '$datatype.model'
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20 #end if
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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21 --branches '$branches'
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22 --chain '$chain_length'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 --burn_in '$burn_in'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 --samples '$samples'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 --parents '$parents'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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26 --min_subs '$min_subs'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 > '$bgm_log'
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 ]]></command>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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29 <inputs>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <conditional name="datatype">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 <param name="value" type="select" label="Type of data">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 <option value="nucleotide">Nucleotide</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 <option value="amino-acid">Amino acid</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 <option value="codon">Codon</option>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 </param>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <when value="nucleotide"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <when value="amino-acid">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 <expand macro="substitution" />
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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41 </when>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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42 <when value="codon">
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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43 <expand macro="gencode" />
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44 </when>
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45 </conditional>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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46 <expand macro="branches"/>
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47 <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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48 <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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49 <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
5
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50 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
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51 <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
0
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52 </inputs>
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53 <outputs>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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54 <data name="bgm_log" format="txt"/>
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55 <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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56 </outputs>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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57 <tests>
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58 <test>
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59 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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60 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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61 <output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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62 </test>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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63 </tests>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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64 <help><![CDATA[
5
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65
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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66 BGM : Bayesian Graphical Models
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67 ===============================
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68
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69 What does this do?
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70 ------------------
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71
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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72 This tools identifies groups of sites in the alignments that experience substitutions along the same branches,
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73 i.g. *co-evolve*.
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74
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75 Brief description
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76 -----------------
823a5afee916 "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 GM (Bayesian Graphical Model) uses a maximum likelihood ancestral state
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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79 reconstruction to map substitution (non-synonymous only for coding data)
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80 events to branches in the phylogeny and then analyzes the joint
823a5afee916 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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81 distribution of the substitution map using a Bayesian graphical model
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82 (network). Next, a Markov chain Monte Carlo analysis is used to generate
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83 a random sample of network structures from the posterior distribution
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84 given the data. Each node in the network represents a site in the
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85 alignment, and links (edges) between nodes indicate high posterior
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86 support for correlated substitutions at the two sites over time, which
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87 implies coevolution.
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88
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89
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90 Input
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91 -----
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92
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93 1. A *FASTA* sequence alignment.
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94 2. A phylogenetic tree in the *Newick* format
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95
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96 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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97
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98 Output
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99 ------
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100
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101 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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102
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103 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BGM for an example)
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104
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105 Further reading
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106 ---------------
1
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107
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108 http://hyphy.org/methods/selection-methods/#BGM
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109
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110
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111 Tool options
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112 ------------
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113 ::
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114
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115 --branches Which branches should be tested for selection?
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116 All [default] : test all branches
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117
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118 Internal : test only internal branches (suitable for
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119 intra-host pathogen evolution for example, where terminal branches
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120 may contain polymorphism data)
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121
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122 Leaves: test only terminal (leaf) branches
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123
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124 Unlabeled: if the Newick string is labeled using the {} notation,
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125 test only branches without explicit labels
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126 (see http://hyphy.org/tutorials/phylotree/)
1
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127
5
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128 --max-parents The maximum number of parents allowed per node, i.e. how many sites
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129 can directly influence substitution patterns at another site
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130 Increasing this number scales complexity nonlinearly
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131 default value: 1
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132
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133 --min-subs The minium number of substitutions per site to include it in the analysis
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134 Filter low complexity (too few substitution) sites
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135 default value: 1
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136
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137 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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138 default value: 5
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139
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140 --steps MCMC chain length (does not apply to Variational-Bayes)
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141 default value: 100,000
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142
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143 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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144 default value: 10,000
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145
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146 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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147 default value: 100
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148
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149
0
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150 ]]></help>
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151 <expand macro="citations">
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152 <citation type="doi">10.1371/journal.pcbi.0030231</citation>
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153 </expand>
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154 </tool>