4ment

phylostan

Phylogenetic inference using Stan

torchtree

A probabilistic framework in PyTorch for phylogenetic models

physher

A multi-algorithmic framework for phylogenetic inference

gradient-benchmark

automatic/analytical differentiation benchmark

flc

Local clock model using relaxed and strict clocks

phylojax

skyplotr

torchtree-bito

beaglepy

hms cutie beagle pie

logstat

torchtree-physher

torchtree-scipy

Package providing extra functionalities from SciPy

torchtree-tensorflow

beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

bioconda-recipes

Conda recipes for the bioconda channel.

bito

Python-interface C++ library implementing subsplit Bayes networks for Bayesian phylogenetics

CBAN

releases of beast2 packaged zip files in a reliable location

docker-images

Repository of Docker images created by Continuum Analytics

dodonaphy-experiments

hamiltorch

PyTorch-based library for Riemannian Manifold Hamiltonian Monte Carlo (RMHMC) and inference in Bayesian neural networks

NUTS

python version of the No-U-Turn Sampler (NUTS) from Hoffman & Gelman, 2011

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

scripts

tippartials

torchtree-experimental

torchtree-experiments

torchtree-notebooks

torchtree-plugin-template

A GitHub template for developing a torchtree plugin

treetime_validation