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Phyletica

Exploring biodiversification.

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Software

Most of my packages, scripts, and other projects are freely available on GitHub. Below are descriptions of a few.

SATé

I am a developer for the software pacakge SATé. SATé is a tool for inferring a sequence alignment and phylogenetic tree using an iterative algorithm. In each iteration, the data set is divided into smaller subproblems by a tree-based decomposition, which are subsequently aligned before being merged back together for phylogenetic tree inference.

dpp-msbayes

dpp-msbayes is a modified version of a popular comparative phylogeographical method for estimating shared evolutionary history in an approximate-Bayesian framework. This version is reparameterized and uses more flexible priors, most notably a Dirichlet-process prior over shared histories. The modifications increase the method’s power for detecting temporal variation in divergences across taxa, allowing for more robust inference that more accurately reflects uncertainty. If you are interested in using this method, it is probably easier (and faster) to use it (and its predecessor) using the Python package PyMsBayes (see below).

PyMsBayes

PyMsBayes is a multi-processing Python API for approximate Bayesian computation (ABC), and provides a multi-processing interface to the comparative phylogeographic software packages, msBayes and dpp-msbayes.

ABACUS

ABACUS (Approximate BAyesian C UtilitieS) is a collection of C utilities for approximate Bayesian computation (ABC). One of the tools distributed with ABACUS is euReject, a program for performing rejection sampling of ABC posteriors.

SeqSift

SeqSift is a python package for downloading, vetting, manipulating, and converting molecular sequence data. It also allows for in silico restriction digests.