MolecularEvolution.jlPhylogenetic Modeling Framework

A Julia package for flexible development of phylogenetic models

Flexible Model Development

Create custom evolutionary models by defining how a process evolves along a branch and get likelihood calculations (and much more) for free! • Mix and match different models on the same phylogeny.

Model Library

Nucleotide, AA, Codon, and generic discrete character models • Continuous models (eg. Brownian motion) • Site- and branch-wise mixture models and more.

Tree Operations

Optimize model parameters, branch lengths, tree topology (NNI), and root position for maximum likelihood inference • Sample from the model and tree posterior with MCMC for Bayesian inference • Infer ancestral states.

Simulation Tools

Sample from a range of realistic phylogenies using a flexible coalescent process • Simulate discrete and continuous data under any model over a simulated or imported phylogeny.