Computational Phylogenetics
... Molecular Data, Evolutionary Modeling and Computational Tools


PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data. We developed a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We further implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models.

The program can be downloaded using the sourceforge repository for the program.


Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N. 2014. Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology. 63(3):349–367.

Silvestro D., Salamin N., Schnitzler J. 2014. Pyrate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution, 5(10):1126–1131.

Written on Tuesday March 4, 2014