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North_American_carnivores 2015-09-05
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                           PyRate
                   version 0.580, May 2015
============================================================

General Info
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PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The method was described here:

Silvestro D., Schnitzler J., Liow L.H., Antonelli A. and Salamin N. (2014) Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology, 63, 349-367.

Silvestro D., Salamin N., Schnitzler J. (2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution, 5, 1126-1131.

Manual and example files can be found here: https://sourceforge.net/projects/pyrate/, a Wiki page is also under construction: https://github.com/dsilvestro/PyRate/wiki. 
The latest version of PyRate can be downloaded here: https://github.com/dsilvestro/PyRate/.

Compatibility and requirements
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PyRate has been tested under Unix operating systems (Mac OS 10.6 or higher and Cent OS 6) and under Windows (XP and 7) using Python 2.6 - 2.7. The program requires the library argparse, which needs to be installed manually under Python 2.6 (it can be found here: https:// code.google.com/p/argparse/), whereas it is part of the default installation in Python 2.7. 

Please note that Python 3.x is currently not supported, Python 2.7.x can be found here: https:// www.python.org/downloads/.

The libraries numpy and scipy are required. Source files and installers are available here: http:// sourceforge.net/projects/numpy/files/ and http://sourceforge.net/projects/scipy/files/. Under UNIX systems, PyRate will use the library multiprocessing and thread (if available) and implement parallel computation of the likelihoods (see command -thread).


Contacts
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Please report suggestions and bugs to:
	pyrate.help[at]gmail.com
Source: README.txt, updated 2015-05-12