Population Genomics Python Packages

pypop-genomics

PyPop: Python for Population Genomics

bamrefine

A small program to mask positions that could result in a PMD artifact from a BAM file using a predefined SNP catalog

sstar

A Python package for detecting archaic introgression from population genetic data with S*

haplodynamics

A python library to develop genomic data simulators

dadi-cli

Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra

timesweeper

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

graphmana

Graph-native data management platform for variant genomics

graphpop-cli

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

relernn

Recombination Landscape Estimation using Recurrent Neural Networks

sai-pg

Statistics for Adaptive Introgression

project-cli-ab3nzac1yc-hatch

Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra