modifiedBPA in DendroPy
Starting with version 3.11.0, DendroPy has an implementation of the modified Brooks Parsimony Analysis algorithm of:
Lieberman, B.S. & Eldredge, N., 1996. " Trilobite biogeography in the Middle Devonian: Geological processes and analytical methods ". Paleobiology, 22(1), p.66-79. ( Mendeley record ).
To run it you have to download DendroPy rather than using the
pip install DendroPy
means of installation. The options for running modified BPA using the geodispersal-analysis.py script are full described in the
README.txt
in DendroPy's
extras/geodispersal
folder.
An example of the installation procedure. Here, is example run on a *nix system (linux, unix, mac os x):
This requires
wget
but
curl
should work. On Windows, you should omit the
set
-x
line and convert the
/
characters to
\
characters (and make sure that you have a tar utility to unpack DendroPy). Otherwise, the procedures should be the same.
Please report bugs to mtholder@ku.edu