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2
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1 Phylomatic (Part of Phylocom)
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2
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3
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4 http://www.phylodiversity.net/phylomatic/phylomatic.html
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5
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6
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7
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8 "The online software takes your list of taxa, and first tries to match them by genus name to the megatree.
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9
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10 Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved.
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11
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12 If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera.
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13
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14 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
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15 (http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
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16 "
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17 http://bioinformatics.oxfordjournals.org/content/24/18/2098
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18
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19
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20 Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution.
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21 Bioinformatics, 24: 2098-2100.
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22
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23
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24 Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB
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25
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26 Included in this package:
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27
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28 * phylomatic - binary file
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29 * phylomatic.pl - wrapper perl script for Galaxy
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30 * phylomatic.xml - Galaxy tool file
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31 * phylomatic_README.txt - documentation file
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32
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33 Installation instruction:
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34
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35 1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy
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36 user account.
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37
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38 2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/
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39 directory.
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40
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41 3. Add the XML information in tool_conf.xml in /galaxy-dist/
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42
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43 4. Restart Galaxy using:
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44
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45 ./run.sh --stop-daemon
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46 ./run.sh --reload --daemon
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47
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48 Known Issues:
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49 Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper
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50 script is used to redirect any warnings generated by the binary file to a log file. |
