Population Genetics Python Packages

fwdpy11

Forward-time simulation in Python using fwdpp

adamixture

Fast population clustering with Adam-EM Optimization.

palos

Misc Python modules developed and used by the yfish group

oppoppopinit

PyPI package containing opposition learning operators and population initializers for evolutionary algorithms

neural-admixture

Rapid population clustering with autoencoders

natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

diploshic

A deep learning tool for identifying hard and soft selective sweeps in population genomic data

haplodynamics

A python library to develop genomic data simulators

mycorrhiza

Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data

gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

timesweeper

Python package for detecting positive selective sweeps using time-series genomics sampling data.

tajimas-d

Compute the Tajima's-D, Pi-Estimator or Watterson-Estimator for multiple sequences.

graphmana

Graph-native data management platform for variant genomics

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

graphpop-cli

GraphPop is a population genomics platform that replaces the flat-file, matrix-based paradigm with a graph-native architecture.

laax

Repository for population genetics and quantitative genetics metrics implementarion and visualization

moranpycess

A general game-theoretical framework to carry out scientific simulations of populations' evolution according to the Moran model 🧮