Tools to work with variant call format files

Recombination Landscape Estimation using Recurrent Neural Networks

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

Population-wide Deletion Calling

rhierbaps: R implementation of hierBAPS

An Efficient Swiss Army Knife for Population Genomic Analyses in R

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

Genome-wide scan for balancing selection using beta statistic

Estimation of population genetic parameters using deep learning

the hierfstat package

PyPop: Python for Population Genomics

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

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

A tool to visualize the haplotype pattern and various information in excel.

Estimation of per-individual inbreeding tracts under a probabilistic framework

Automated and distributed population genetic model inference from allele frequency spectra

starmie: plotting and inference for population structure models 🌟

Multisample Variant Format ToolKit