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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">
2 <description>Pairwise distance between taxa in a phylogenetic tree</description>
3 <requirements>
4 <requirement type="perl-module">Bio</requirement>
5 </requirements>
6 <command interpreter="perl">
7 PD.pl $intable $intree $outtable $half
8 </command>
9 <inputs>
10 <param name="intree" type="data" format="txt" label="Input Tree File" help="newick" />
11 <param name="intable" type="data" format="tabular" label="Table of species pairs" help="species tab species" />
12 <param name='half' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Calculate Divergence times (divides pairwise distances in half)' />
13 </inputs>
14 <outputs>
15 <data format="tabular" name="outtable" label="${tool.name} on ${on_string}: Out file" />
16 </outputs>
17 <help>
18 **What it does**
19
20 PDpairs generates Phylogenetic Distances (PD) for pairs of species in a phylogenetic tree.
21
22 ------
23
24 **Input formats**
25
26 Input a table of species pairs::
27
28 species1 species2
29 species2 species4
30
31 And a Newick format phylogeny with branch lengths
32
33 ------
34
35 **Outputs**
36
37 Output is a table of the species pairs followed by a column of pairwise distance for each tree in the file::
38
39 species1 species2 1.104
40 species2 species4 2.119
41
42 -------
43
44 **Citations**
45
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.
47
48 Current Osiris Citation is here
49
50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
51
52 Additional Citations for this tool
53
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.
55
56 Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1-10.
57
58 </help>
59 </tool>