Mercurial > repos > iuc > phyml

annotate phyml.xml @ 1:2677a6dae0e0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
author iuc
date Mon, 20 Jan 2020 17:45:35 +0000
parents a9ee99c3be94
children 19becf767d4f
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2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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1 <tool id="phyml" name="PhyML" version="3.3.20190321">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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2 <description>Phylogeny software based on the maximum-likelihood</description>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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3 <requirements>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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4 <requirement type="package" version="3.3.20190321">phyml</requirement>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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5 </requirements>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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6 <version_command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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7 <![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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8 </version_command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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9 <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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10 <![CDATA[
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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11 ##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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12 ln -sf '$input' '${input.name}' &&
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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13 #if $userInputTree:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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14 ln -sf '${$userInputTree}' '${$userInputTree.name}' &&
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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15 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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16
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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17 phyml --input '${input.name}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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18 '${phylip_format}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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19 --datatype '${seq.type_of_seq}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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20 --multiple '${nb_data_set}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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21
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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22 #if (str($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"
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23 --bootstrap '${support_condition.branchSupport}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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24 #else:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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25 --bootstrap '${support_condition.branchSupport.replicate}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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26 #end if
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 $seq.type_of_seq == "nt":
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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29 -t '${seq.tstv}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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30 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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31
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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32 --model '${seq.model}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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33 -f '${equi_freq}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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34 --pinv '${prop_invar}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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35
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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36 --nclasses '${nbSubstCat}'
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 #if (str($nbSubstCat) != "1"):
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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39 --alpha '${gamma}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
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40 #end if
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 --search '${move}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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43 -o '${optimisationTopology}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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44
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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45 #if $userInputTree:
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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46 --inputtree '${$userInputTree.name}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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47 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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48
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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49 #if $numStartSeed != "0":
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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50 --r_seed '${numStartSeed}'
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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51 #end if
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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52
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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53 --no_memory_check > '${output_stdout}' &&
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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54 grep 'failed' '${output_stdout}' >&2;
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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55 ]]>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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56 </command>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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57 <inputs>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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58 <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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59 <param name="phylip_format" type="select" label="Changes interleaved format">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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60 <option value="">Interleaved</option>
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61 <option value="--sequential">Sequential</option>
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62 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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63 <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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64 <conditional name="seq">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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65 <param name="type_of_seq" type="select" label="Data type">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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66 <option value="nt">Nucleic acids</option>
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67 <option value="aa">Amino acids</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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68 </param>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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69 <when value="nt">
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70 <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" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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71 <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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72 <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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73 <option value="JC69">JC69</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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74 <option value="K80">K80</option>
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75 <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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76 <option value="F84">F84</option>
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77 <option value="TN93">TN93</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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78 <option value="GTR">GTR</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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79 </param>
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80 </when>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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81 <when value="aa">
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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82 <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"
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83 <option value="LG">LG</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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84 <option value="WAG">WAG</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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85 <option value="JTT">JTT</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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86 <option value="MtREV">MtREV</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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87 <option value="Dayhoff">Dayhoff</option>
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parents: 0
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88 <option value="DCMut">DCMut</option>
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parents: 0
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89 <option value="RtREV">RtREV</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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90 <option value="CpREV">CpREV</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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91 <option value="VT">VT</option>
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parents: 0
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92 <option value="Blosum62">Blosum62</option>
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parents: 0
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93 <option value="MtMam">MtMam</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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94 <option value="MtArt">MtArt</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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95 <option value="HIVw">HIVw</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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96 <option value="HIVb">HIVb</option>
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parents: 0
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97 </param>
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parents: 0
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98 </when>
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parents: 0
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99 </conditional>
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parents: 0
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100 <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"/>
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parents: 0
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101 <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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102 <option value="m">ML/Model</option>
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103 <option value="e">Empirical</option>
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parents: 0
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104 </param>
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parents: 0
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105 <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"
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106 <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"
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parents: 0
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107 <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"
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parents: 0
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108 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
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parents: 0
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109 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
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110 <option value="BEST">Best of NNI and SPR</option>
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parents: 0
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111 </param>
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parents: 0
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112 <param name="optimisationTopology" type="select" label="Optimise topology">
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113 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
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114 <option value="tl">Tree topology, Branch length</option>
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parents: 0
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115 <option value="l">Branch length</option>
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parents: 0
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116 <option value="r">Rate parameter</option>
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117 <option value="n">No parameter is optimized</option>
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parents: 0
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118 </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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119 <conditional name="support_condition">
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120 <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"
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121 <option value="0">No bootstrap</option>
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122 <option value="1">Bootstrap</option>
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parents: 0
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123 <option value="-1">likelihood aLRT statistics</option>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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124 <option value="-2">likelihood Chi2-based</option>
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125 <option value="-4" selected='true'>SH-like</option>
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parents: 0
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126 <option value="-5">Approximate Bayes branch supports</option>
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127 </param>
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parents: 0
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128 <when value="0"/>
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parents: 0
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129 <when value="-1"/>
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parents: 0
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130 <when value="-2"/>
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131 <when value="-4"/>
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132 <when value="-5"/>
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133 <when value="1">
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134 <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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135 </when>
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136 </conditional>
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137 <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"
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138 <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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139 </inputs>
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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140 <outputs>
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141 <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"
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142 <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"
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143 <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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144 </outputs>
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145 <tests>
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146 <test>
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147 <param name="input" value="phylip" />
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148 <param name="prop_invar" value="0"/>
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149 <param name="type_of_seq" value="nt" />
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150 <param name="numStartSeed" value="1458308600" />
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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151 <output name="output_tree">
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152 <assert_contents>
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153 <has_text text="Rhes_cDNA:0.0"/>
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154 <has_text text="Baboon:0.0"/>
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155 <has_text text="Orangutan:0.0"/>
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156 <has_text text="Gibbon:0.0"/>
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157 <has_text text="Human:0.0"/>
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158 <has_text text="Chimp:0.0"/>
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159 </assert_contents>
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160 </output>
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161 <output name="output_stats" file="phylip_phyml_stats.txt" lines_diff="4"/>
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162 </test>
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163 </tests>
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164 <help>
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165 <![CDATA[
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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166 .. class:: infomark
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167
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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168 #########
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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169 PhyML 3.3
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170 #########
2677a6dae0e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
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171
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172 A simple, fast, and accurate algorithm to estimate
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173 large phylogenies by maximum likelihood''
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174
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175 ==========
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176 Overview:
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177 ==========
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178
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179 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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180
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181 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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182
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183 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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184
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185 -----
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186
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187
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188 For further informations, please visite the PhyML_ website.
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189
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190 .. _PhyML: http://www.atgc-montpellier.fr/phyml/
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191
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192 Please cite this paper if you use this software in your publications.
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193
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194
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195 ]]>
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196 </help>
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197 <citations>
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198 <citation type="doi">10.1093/sysbio/syq010</citation>
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199 </citations>
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200 </tool>