Population Genetics Python Packages

fwdpy11

Forward-time simulation in Python using fwdpp

adamixture

Fast population genetics clustering.

oppoppopinit

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

clawbio

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

neural-admixture

Rapid population clustering with autoencoders

palos

Misc Python modules developed and used by the yfish group

diploshic

feature-based deep learning for the identification of selective sweeps

gnomad-db

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

natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

mycorrhiza

Mycorrhiza population assignment tools.

haplodynamics

A python library to develop genomic data simulators

poppunk

PopPUNK (POPulation Partitioning Using Nucleotide Kmers)

tajimas-d

Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.

timesweeper

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

graphpop-cli

Graph database-native population genomics CLI with O(V*K) complexity

graphmana

Graph-native data management platform for population genomics

moranpycess

Python framework for Moran Processes driven by game theory

laax

Local Ancestry Analysis in Crossbred Populations