Mercurial > repos > iuc > phyml

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:57:13 +0000
parents 19becf767d4f
children
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19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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1 <tool id="phyml" name="PhyML" version="@VERSION@">
3
7c44ad3ab06c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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2 <description>Phylogeny software based on the maximum-likelihood method</description>
7c44ad3ab06c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <xrefs>
7c44ad3ab06c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <xref type="bio.tools">phyml</xref>
7c44ad3ab06c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 </xrefs>
2
19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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6 <macros>
19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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7 <token name="@VERSION@">3.3.20190909</token>
19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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8 </macros>
1
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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9 <requirements>
2
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10 <requirement type="package" version="@VERSION@">phyml</requirement>
1
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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11 </requirements>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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12 <version_command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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13 <![CDATA[ phyml --version ]]>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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14 </version_command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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15 <command detect_errors="default">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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16 <![CDATA[
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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17 ##PhyML outputs are based on input path and we need to create outputs in working_dir.
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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18 ln -sf '$input' '${input.name}' &&
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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19 #if $userInputTree:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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20 ln -sf '${$userInputTree}' '${$userInputTree.name}' &&
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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21 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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22
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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23 phyml --input '${input.name}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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24 '${phylip_format}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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25 --datatype '${seq.type_of_seq}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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26 --multiple '${nb_data_set}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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27
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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28 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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29 --bootstrap '${support_condition.branchSupport}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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30 #else:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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31 --bootstrap '${support_condition.branchSupport.replicate}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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32 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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33
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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34 #if $seq.type_of_seq == "nt":
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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35 -t '${seq.tstv}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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36 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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37
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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38 --model '${seq.model}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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39 -f '${equi_freq}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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40 --pinv '${prop_invar}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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41
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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42 --nclasses '${nbSubstCat}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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43
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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44 #if (str($nbSubstCat) != "1"):
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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45 --alpha '${gamma}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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46 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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47
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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48 --search '${move}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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49 -o '${optimisationTopology}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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50
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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51 #if $userInputTree:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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52 --inputtree '${$userInputTree.name}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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53 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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54
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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55 #if $numStartSeed != "0":
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56 --r_seed '${numStartSeed}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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57 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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58
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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59 --no_memory_check > '${output_stdout}' &&
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60 grep 'failed' '${output_stdout}' >&2;
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61 ]]>
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62 </command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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63 <inputs>
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64 <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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65 <param name="phylip_format" type="select" label="Changes interleaved format">
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66 <option value="">Interleaved</option>
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67 <option value="--sequential">Sequential</option>
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68 </param>
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69 <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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70 <conditional name="seq">
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71 <param name="type_of_seq" type="select" label="Data type">
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72 <option value="nt">Nucleic acids</option>
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73 <option value="aa">Amino acids</option>
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74 </param>
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75 <when value="nt">
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76 <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" />
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77 <param name="model" type="select" label="Substitution model">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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78 <option value="HKY85">HKY85</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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79 <option value="JC69">JC69</option>
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80 <option value="K80">K80</option>
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81 <option value="F81">F81</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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82 <option value="F84">F84</option>
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83 <option value="TN93">TN93</option>
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84 <option value="GTR">GTR</option>
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85 </param>
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86 </when>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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87 <when value="aa">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
88 <param name="model" type="select" label="Evolution model">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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89 <option value="LG">LG</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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90 <option value="WAG">WAG</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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91 <option value="JTT">JTT</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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92 <option value="MtREV">MtREV</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
93 <option value="Dayhoff">Dayhoff</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
94 <option value="DCMut">DCMut</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
95 <option value="RtREV">RtREV</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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96 <option value="CpREV">CpREV</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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97 <option value="VT">VT</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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98 <option value="Blosum62">Blosum62</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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99 <option value="MtMam">MtMam</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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100 <option value="MtArt">MtArt</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
101 <option value="HIVw">HIVw</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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102 <option value="HIVb">HIVb</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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103 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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104 </when>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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105 </conditional>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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106 <param name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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107 <param name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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108 <option value="m">ML/Model</option>
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parents: 0
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109 <option value="e">Empirical</option>
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parents: 0
diff changeset
110 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
111 <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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112 <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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113 <param name="move" type="select" label="Tree topology search">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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114 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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115 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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116 <option value="BEST">Best of NNI and SPR</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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117 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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118 <param name="optimisationTopology" type="select" label="Optimise topology">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
119 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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120 <option value="tl">Tree topology, Branch length</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
121 <option value="l">Branch length</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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122 <option value="r">Rate parameter</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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123 <option value="n">No parameter is optimized</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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124 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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125 <conditional name="support_condition">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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126 <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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127 <option value="0">No bootstrap</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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128 <option value="1">Bootstrap</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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129 <option value="-1">likelihood aLRT statistics</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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130 <option value="-2">likelihood Chi2-based</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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131 <option value="-4" selected='true'>SH-like</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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132 <option value="-5">Approximate Bayes branch supports</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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133 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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134 <when value="0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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135 <when value="-1"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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136 <when value="-2"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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137 <when value="-4"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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138 <when value="-5"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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139 <when value="1">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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140 <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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141 </when>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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142 </conditional>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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143 <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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144 <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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145 </inputs>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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146 <outputs>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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147 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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148 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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149 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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150 </outputs>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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151 <tests>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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152 <test>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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153 <param name="input" value="phylip" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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154 <param name="prop_invar" value="0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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155 <param name="type_of_seq" value="nt" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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156 <param name="numStartSeed" value="1458308600" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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157 <output name="output_tree">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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158 <assert_contents>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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159 <has_text text="Rhes_cDNA:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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160 <has_text text="Baboon:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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161 <has_text text="Orangutan:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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162 <has_text text="Gibbon:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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163 <has_text text="Human:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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164 <has_text text="Chimp:0.0"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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165 </assert_contents>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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166 </output>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
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167 <output name="output_stats" file="phylip_phyml_stats.txt" lines_diff="4"/>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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168 </test>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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parents: 0
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169 </tests>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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170 <help>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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171 <![CDATA[
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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172 .. class:: infomark
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173
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174 #########
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175 PhyML 3.3
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176 #########
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177
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178 A simple, fast, and accurate algorithm to estimate
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179 large phylogenies by maximum likelihood''
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180
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181 ==========
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182 Overview:
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183 ==========
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184
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185 PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued.
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186
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187 We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task.
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188
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189 It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.
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190
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191 -----
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192
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193
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194 For further informations, please visite the PhyML_ website.
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195
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196 .. _PhyML: http://www.atgc-montpellier.fr/phyml/
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197
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198 Please cite this paper if you use this software in your publications.
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199
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200
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201 ]]>
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202 </help>
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203 <citations>
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204 <citation type="doi">10.1093/sysbio/syq010</citation>
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205 </citations>
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206 </tool>