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normalizing_flows

Pytorch implementations of density estimation algorithms: BNAF, Glow, MAF, RealNVP, planar flows

phast

PHAST

phylo_structural_em

Structural Expectation Maximization algorithm for phylogenetic inference

phyloinfer

Developing efficient Bayesian phylogenetic inference methods

phylostan

Phylogenetic inference using Stan

physher

Phylogenetic analysis of genetic data

pytorch-vae

A Collection of Variational Autoencoders (VAE) in PyTorch.

pytorch_mlr

A modern implementation of Multinomial Logistic Regression with SGD training

pyvolve

Python library to simulate evolutionary sequence data

quasirecomb

Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).

sbn

Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks

scholarly

Retrieve author and publication information from Google Scholar in a friendly, Pythonic way

seq-gen

Sequence simulator

slm_kgenomvir

Evaluation of Statistical Linear Models for Genome Virus Classification

theano-recurrence

Recurrent Neural Networks (RNN, GRU, LSTM) and their Bidirectional versions (BiRNN, BiGRU, BiLSTM) for word & character level language modelling in Theano

torchtree

A probabilistic framework in PyTorch for phylogenetic models

tree_pruner

pruner: Implementing the Felsenstein's Tree Pruning algorithm

uqam_bif7101

vae-clustering

Unsupervised clustering with (Gaussian mixture) VAEs

variational-autoencoder

Variational autoencoder implemented in tensorflow and pytorch (including inverse autoregressive flow)

vbpi-nf

Code for improved variational Bayesian phylogenetic inference with normalizing flows

vbpi-torch

Pytorch Implementation of Variational Bayesian Phylogenetic Inference

vbsky

Variational Bayesian skyline infers evolutionary models from large amounts of phylogenetic data.

vcsmc

Variational Combinatorial Sequential Monte Carlo methods for Bayesian Phylogenetic Inference