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Diversification Rate Software Links

Please contact me if you know of relevant programs not listed below.

APE is a versatile software package written in R by Emmanuel Paradis at the Université Montpellier that implements a number of features for investigating differential diversification rates, such as generating lineage-through-time plots, estimating absolute diversification rates, and implementing temporal methods (based on survival analysis under a pure birth process) to detect significant decreases in diversification rate through time and identify significant variation in diversification rate across lineages. APE requires installation of R, which has been compiled for Mac OS X, Windows, and several Linux distributions.
Bi-De is a phylogeny simulation program written by Andrew Rambaut at University of Edinburgh that models diversification under a generalized birth-death process that allows the user to specify periods of epidemic, endemic, or custom-function growth, induce episodes of mass extinction, and stipulate sampling intensity. The simulated histories are output as lineage-through-time plots which may be compared to plots derived from empirical data. Bi-De has largely been superceded by Phyl-O-Gen, but remains available either as a Mac OS 7-9 executable.
Diverse is a module for the Mesquite program written by Wayne Maddison that implements the likelihood approach proposed by Maddison, Midford & Otto (2007) for evaluating associations between the state of a binary character and rates of speciation and extinction. This method is particularly useful for situations in which there is reason to suspect that a preponderance of species exhibit a given trait because of asymmetric transition probabilities between states. Diverse is a GUI program that will run on any platform that supports the Java Virtual Machine.


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