Open source software powers basic science.

automated phylogeography

Scripts used in automated phylogeographic analysis of bat data. These scripts are from submission JBI-17-0676.


PHylogeographic infeRence using APproximate Likelihoods (PHRAPL) is funded by the National Science Foundation and developed in collaboration with the Brian O'Meara lab.

spedeSTEM 1.0

The original version of spedeSTEM is the one to use, provided you have access to PAUP*. spedeSTEM was funded by the National Science Foundation


P2C2M is an R package that allows users to assess the fit of the multispecies coalescent model to their empirical data.

Carstens et al. (2013) scripts

Scripts used in the processing of Salix melanopsis genomic data are available here

spedeSTEM 2.0

spedeSTEM was rewritten using Python as part of a project for a couple of former undergraduate researchers. This version is ideal for researchers who want to estimate gene trees prior to the analysis, but use a Linux or UNIX-based OS. Examples files and a tutorial are also available.

Reid et al. (2014) *Beast PPS

The scripts for posterior predictive simulation described by Reid et al. 2014 are available here. Note that P2C2M is an updated version of these scripts.

Tsai & Carstens (2013) scripts

For those interested in the scripts and the map from Tsai and Carstens (2013).


An R package to conduct a bayesian version of the GMYC analysis was written by Noah Reid.


A PERL program to assemble and align genomic data described by Hird et al. (2012).

Hird et al. (2010) scripts

For those interested in the scripts from Hird et al. (2010).


Software to conduct a Community tree analysis is now available.

IMa information theory

An excel file demonstrates how we calculated the model probabilities using IMa described by Carstens et al. (2009).


We make inferences about the history of species and ecological communities using genetic, environmental and morphological data. We conduct investigations in a range of organisms: bats, insects, carnivorous plants, salamanders, willows, spiders, snails, slugs and viruses.

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