Population Genetics Python Packages

fwdpy11

Forward-time simulation in Python using fwdpp

natal-core

Numerical Aggregation Toolkit for Analysis of Lifecycles

adamixture

Fast population genetics clustering.

snputils

Python toolkit for fast genotype I/O, ancestry analysis, population-genetics statistics, genotype QC, GWAS, and visualization

oppoppopinit

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

neural-admixture

Rapid population clustering with autoencoders

manifold-genetics

An end-to-end pipeline from PLINK genotypes to publication-ready visualizations.

palos

A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).

diploshic

feature-based deep learning for the identification of selective sweeps

clawbio

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

ldetect-lite

Fast calculation of approximately independent linkage disequilibrium blocks

fasta2genotype

Convert STACKS fasta to many genotype formats

mycorrhiza

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

haplodynamics

A python library to develop genomic data simulators

gnomad-db

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

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

tajimas-d

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

timesweeper

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

fastrho

Fine-scale recombination maps from population genotypes, without per-dataset training.

graphpop-cli

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

graphmana

Graph-native data management platform for variant genomics

moranpycess

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