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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="PDpairs" name="PDpairs">
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2 <description>Pairwise distance between taxa in a phylogenetic tree</description>
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3 <requirements>
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4 <requirement type="perl-module">Bio</requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 PD.pl $intable $intree $outtable $half
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8 </command>
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9 <inputs>
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10 <param name="intree" type="data" format="txt" label="Input Tree File" help="newick" />
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11 <param name="intable" type="data" format="tabular" label="Table of species pairs" help="species tab species" />
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12 <param name='half' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Calculate Divergence times (divides pairwise distances in half)' />
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="outtable" label="${tool.name} on ${on_string}: Out file" />
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16 </outputs>
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17 <help>
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18 **What it does**
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19
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20 PDpairs generates Phylogenetic Distances (PD) for pairs of species in a phylogenetic tree.
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21
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22 ------
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23
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24 **Input formats**
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25
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26 Input a table of species pairs::
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27
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28 species1 species2
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29 species2 species4
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30
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31 And a Newick format phylogeny with branch lengths
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32
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33 ------
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34
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35 **Outputs**
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36
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37 Output is a table of the species pairs followed by a column of pairwise distance for each tree in the file::
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38
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39 species1 species2 1.104
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40 species2 species4 2.119
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41
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42 -------
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43
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44 **Citations**
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45
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46 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
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47
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48 Current Osiris Citation is here
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49
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50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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51
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52 Additional Citations for this tool
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53
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54 Stajich, J., Block, D., Boulez, K., Brenner, S., Chervitz, S., Dagdigian, C., Fuellen, G., Gilbert, J., Korf, I., Lapp, H. et al. (2002). The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12,1611 -1618.
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55
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56 Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1-10.
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57
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58 </help>
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59 </tool>