Rate Software Links
Please contact me
if you know of relevant programs not listed below.
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
Mac OS X, Windows, and several Linux distributions.
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
Phyl-O-Gen, but remains available either as a Mac OS 7-9 executable.
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.