dsilvestro

PyRate

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

LiteRate

Fast estimation of immigration, birth and death rates from large datasets using reversible jump MCMC

npBNN

Bayesian neural networks using Numpy and Scipy

rootBBB

Clade age estimation using a Bayesian Brownian bridge model

fossilBM

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

ruNNer

Train and run neural networks in Python

mcmc-diversitree

This repository includes Bayesian implementations of the MuSSE and ClaSSE methods. The use of (half-Cauchy or Exponential) hyper-priors on the rate parameters allows to control for overparameterization.

raxmlGUI

raxmlGUI 2.0 is now available: A new graphical interface for RAxML

iucn_sim_dev

A program for estimating extinction probability and date for a given set of species, based on IUCN threat assessments

ProvenanceFinder

Probabilistic estimation of the source of origin of sediments

agez

Age estimation from zircon samples

gdgt-ai

Estimation of climatic variables using GDGT data and neural networks

macroevolution_practicals

micro2macroEvolution

Forward individual-based simulations of evolution to link microevolutionary processes to macroevolution

UMAP_scripts