PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.

Bayesian inference of trait evolution under a “fossilized” Brownian motion.

A Julia interface to the Paleobiology Database (PBDB) data service.

Data and analyses used in Moon & Stubbs, Communications Biology doi:10.1038/s42003-020-0779-6

Data and code for "The Cultural Macroevolution of Arcade Video Games: Innovation, Collaboration, and Collapse"

Data, code & figures used to assess global patterns of potential thermal niche filling

Paper - A novel function of banded stripes to prevent cannibalism in snake-eating snakes

Benchmarks Physics-Informed Neural ODEs vs. Fine-Tuned Foundation Models (Chronos) on Cenozoic fossil data. Includes a Random Forest analysis of the Lilliput Effect to test climate vs. taphonomy drivers. Results show Neural ODEs outperform generic Transformers (MSE 13.05) in reconstructing deep-time evolutionary history.

Galapagos Islands Testudinidae Macroevolution (GITM)

Macroevolutionary analyses of the Monodoreae tribe (Annonaceae) 🧬🌳🌍

Infer phylogeny parameters with Deep Learning.

This repository provides research data and source code for reproducing the computational analysis reported in the manuscript "Community-level functional stability in East African herbivores amid major environmental change"

Supplementary code and data for "The paradox of predictability"

R scripts to explore global patterns of diversificatio and species richness of current and present-natural mammals

This repository contains the R code, data, and figures for the paper Vidal-García, M., O'Hanlon, J.C., Svenson, G.J, Umbers, K.D.L. (in press) The evolution of defensive displays in praying mantises. Proceedings of the Royal Society B

Code and data to reproduce all analyses and figures in Hill et al 2023

R code and analysis for Bazzi et al. (2025)

Paper - Best practices for building and curating databases for comparative analyses