population-genetics

An analysis and visualization platform for 'omics data

An open-source toolkit for large-scale genomic analysis

Tools to work with variant call format files

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

A library for working with phylogenetic and population genetic data.

feature-based deep learning for the identification of selective sweeps

deep learning prediction of geographic location from individual genome sequences

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Fast calculations of linkage-disequilibrium in large-scale human cohorts

Population genetic simulations in R 🌍

LDlinkR

Causal Mixture Model for GWAS summary statistics

rhierbaps: R implementation of hierBAPS