bold-phylodiv-scripts

Scripts to calculate phylodiversity and its distribution from BOLD DNA barcode data.

Usage

Call the PHP script phylodiv.php from the PHP executable with a taxon name and optionally other arguments.

E.g. path/to/php phylodiv.php Hexactinellida 10 15 15 path/to/clustalw2 path/to/paup

List of command line arguments:

1. Taxonomic name of the group to analyze.
   • At phylum, order, class, family, subfamily or genus level, or species binomial. E.g. Lachninae, E.g. Pandion%20haliaetus
   • If there are spaces, enclose the argument in quotes " " or replace spaces with URI encoding character %20
2. Optionally, the number of subsamples to take from sequences obtained.
   • Default = 20.

Optionally, the size of the grid squares to separate sequences by:

3. Latitude (width) of grid squares
   • Default = 30
4. Longitude (height) of grid squares
   • Default = 30
5. Optionally, the path to the Clustal executable.
   • Default = \"Program Files (x86)"\ClustalW2\clustalw2 on windows, and /usr/local/bin/clustalw2 otherwise
6. Optionally, the path to the PAUP executable.
   • Default = %appdata%\PAUP4\paup4 on windows, and /usr/local/bin/paup otherwise