Mercurial > repos > iuc > fasttree

annotate fasttree.xml @ 0:a415bf349f95 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
author iuc
date Mon, 19 Feb 2018 11:36:06 -0500
parents
children 72ad35752216
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0
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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2 <tool id="fasttree" name="FASTTREE" version="@VERSION@">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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3 <description>adjust short reads</description>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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4 <macros>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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5 <token name="@VERSION@">2.1.10</token>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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6 </macros>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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7 <requirements>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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8 <requirement type="package" version="@VERSION@">FastTree</requirement>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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9 </requirements>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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10 <version_command>FastTree</version_command>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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11 <command detect_errors="aggressive">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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12 <![CDATA[
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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13 FastTree
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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14
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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15 $model_selector.format
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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16 $model_selector.model
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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17 -nopr
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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18 #if $input_selector.select_format == 'fasta':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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19 $input_selector.quote
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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20 #else if $input_selector.select_format == 'phylip':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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21 -n $input_selector.num
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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22 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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23 #set $inform = $input_selector.intree_selector.intree_format
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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24 #if $inform == 'one':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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25 -intree1 '$input_selector.intree_selector.start_tree'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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26 #else if $inform == 'many':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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27 -intree '$input_selector.intree_selector.start_tree'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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28 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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29 #if $advanced_selector.maximize == 'max':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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30 #if $advanced_selector.cat_selector.conrate == 'no':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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31 -cat $advanced_selector.cat_selector.ratecat
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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32 #else if $advanced_selector.cat_selector.conrate == 'yes':
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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33 -nocat
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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34 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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35 $advanced_selector.gamma
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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36 $advanced_selector.nosupport
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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37 $advanced_selector.mllen
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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38 $advanced_selector.likelihood
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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39 $advanced_selector.fastest
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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40 $advanced_selector.pseudo
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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41 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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42
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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43 < '$input' > '$output'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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44
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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45 #if $save_logfile:
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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46 2> '$log'
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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47 #end if
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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48
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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49 ]]>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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50 </command>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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51 <inputs>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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52 <conditional name="input_selector">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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53 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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54 <option value="fasta" selected="true">fasta</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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55 <option value="phylip">phylip</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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56 </param>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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57 <when value="fasta">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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58 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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59 <param name="quote" argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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60 <conditional name="intree_selector">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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61 <param name="intree_format" type="select" label="Set starting tree(s)">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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62 <option value="none" selected="true">No starting trees</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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63 <option value="one">Use starting tree</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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64 </param>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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65 <when value="none">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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66 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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67 <when value="one">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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68 <param format="nhx" name="start_tree" type="data" label="Newick file" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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69 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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70 </conditional>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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71 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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72 <when value="phylip">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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73 <param format="phylip" name="input" type="data" label="PHYLIP file" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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74 <param name="num" type="integer" value="1" optional="true" label="Number of multiple alignments" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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75 <conditional name="intree_selector">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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76 <param name="intree_format" type="select" label="Set starting tree(s)">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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77 <option value="none" selected="true">No starting trees</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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78 <option value="one">One tree for multiple alignments</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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79 <option value="many">Multiple trees for multiple alignments</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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80 </param>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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81 <when value="none">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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82 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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83 <when value="one">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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84 <param format="nhx" name="start_tree" type="data" multiple="false" label="Newick file" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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85 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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86 <when value="many">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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87 <param format="nhx" name="start_tree" type="data" label="Newick file" multiple="false" help="The tree produced by the full alignment to be used as a starting point for each bootstrapping replicate. This will save considerable computation time." />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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88 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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89 </conditional>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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90 </when>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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91 </conditional>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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92 <param name="save_logfile" type="boolean" truevalue="" falsevalue="" checked="false" label="Save log file output" />
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
parents:
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93 <conditional name="model_selector">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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94 <param name="format" type="select" label="Protein or nucleotide alignment" help="Specify if the aligned sequences are nucleotide or protein sequences">
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95 <option value="-nt">Nucleotide</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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96 <option value="" selected="true">Protein</option>
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97 </param>
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98 <when value="-nt">
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99 <param name="model" type="select" label="Nucleotide evolution model">
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100 <option value="-gtr" selected="true">GTR+CAT</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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101 <option value="">Jukes-Cantor + CAT</option>
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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102 </param>
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103 </when>
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104 <when value="">
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105 <param name="model" type="select" label="Protein evolution model">
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
iuc
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106 <option value="" selected="true">JTT + CAT</option>
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107 <option value="-wag">WAG + CAT</option>
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108 <option value="-lg">LG + CAT</option>
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109 </param>
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110 </when>
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111 </conditional>
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112 <conditional name="advanced_selector">
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113 <param name="maximize" type="select" label="Show advanced options">
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114 <option value="min" selected="true">No</option>
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115 <option value="max">Yes</option>
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116 </param>
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117 <when value="min">
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118 </when>
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119 <when value="max">
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120 <conditional name="cat_selector">
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121 <param name="conrate" type="select" label="Use constant rates?">
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122 <option value="no" selected="true">Do not use constant rates.</option>
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123 <option value="yes">Use constant rates.</option>
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124 </param>
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125 <when value="no">
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126 <param name="ratecat" type="integer" value="20" label="Specify the number of rate categories of sites (default 20)" />
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127 </when>
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128 <when value="yes">
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129 </when>
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130 </conditional>
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131 <param value="gamma" argument="-gamma" type="boolean" truevalue="-gamma" falsevalue="" checked="false" label="Use Gamma20" help="After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood." />
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132 <param value="nosupport" argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue="" checked="false" label="Eliminates the support value computation. Support value computation is not recommended for wide alignments."/>
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133 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." />
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134 <param name="fastest" argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" />
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135 <param name="pseudo" argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." />
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136 <param name="mllen" argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." />
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137 </when>
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138 </conditional>
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139 </inputs>
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140 <outputs>
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141 <data name="output" format="nhx" label="${tool.name} on ${on_string}:tree.nhx" />
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142 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt">
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143 <filter>save_logfile</filter>
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144 </data>
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145 </outputs>
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146 <tests>
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147 <test>
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148 <param name="select_format" value="fasta" />
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149 <param name="model" value="" />
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150 <param name="input" value="aligned.fasta" />
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151 <param name="format" value="-nt" />
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152 <param name="save_logfile" value="true" />
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153 <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" />
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154 <output name="log" file="log.txt" ftype="txt" compare="contains" />
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155 </test>
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156 </tests>
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157 <help>
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158 <![CDATA[
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159
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160 ===========
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161 Description
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162 ===========
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163
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164 .. class:: infomark
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165
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166 FastTree_ infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software.
a415bf349f95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit e47dfac91821500d0fcfc43750d036662c7c43ca
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167
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168 .. _FastTree: http://meta.microbesonline.org/fasttree
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169
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170 -----
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171
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172 -----
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173 Input
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174 -----
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175
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176 A) Aligned sequences file in FASTA format (e.g. the alignment from the 'PyNAST' tool) or PHYLIP format.
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177 B) Newick file to set the starting tree(s) (optional)
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178
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179 ----------
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180 Parameters
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181 ----------
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182
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183 Nucleotide or protein alignment
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184 To specify the type of sequence alignment (nucleotide or protein) you are providing.
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185
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186 Nucleotide evolution model
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187 Specify GTR+CAT (Generalized Time Reversable Model) or Jukes-Cantor + CAT.
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188
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189 Protein evolution model
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190 Specify JTT (Jones-Taylor-Thornton 1992 model) + CAT, WAG (Whelan-And-Goldman 2001 model) + CAT, or LG (Le-Gascuel 2008 model) + CAT.
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191
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192 Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree. (fasta only)
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193 FastTree will not be able to read these trees back in. (-quote)
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194
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195 Number of multiple alignments (phylip only)
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196 (-n)
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197
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198 -------------------
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199 Advanced Parameters
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200 -------------------
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201
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202 Number of rates of sites
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203 Defaults to 20. Specify whether you wish to choose constant rates. (-cat/-nocat)
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204
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205 Use Gamma20
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206 After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood. (-gamma)
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207
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208 Eliminates the support value computation. Support value computation is not recommended for wide alignments.
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209 (-nosupport)
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210
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211 Turn off maximum-likelihood.
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212 (-noml)
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213
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214 Speed up the neighbor joining phase and reduce memory usage
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215 Recommended for >50,000 sequences. (-fastest)
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216
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217 Use pseudocounts
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218 Recommended if you have many fragmentary sequences. (-pseudo)
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219
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220 Optimize branch lengths without ML NNIs.
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221 (-mllen)
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222
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223 ------
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224 Output
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225 ------
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226
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227 This tool produces two output files, one of which is optional (the log file).
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228
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229 (A) The phylogenetic tree in Newick_ format (nhx).
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230
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231 (B) *(optional)* The log file, containing information of the FastTree run to build the phylogenetic tree.
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232
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233 .. class:: infomark
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234
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235 The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences.
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236
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237 .. _Newick: http://en.wikipedia.org/wiki/Newick_format
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238
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239 -----
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240
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241
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242 =========
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243 Resources
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244 =========
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245
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246 FastTree_v2.1.10_
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247
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248 .. _FastTree_v2.1.10: http://meta.microbesonline.org/fasttree/#Install
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249 ]]>
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250 </help>
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251 <citations>
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252 <citation type="doi">10.1371/journal.pone.0009490</citation>
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253 </citations>
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254 </tool>