RADseq Data Exploration, Manipulation and Visualization using R

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

stackr: an R package to run stacks software pipeline

command-line tools for the management of genotype likelihoods and allele counts

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Genotyping of segregating mobile elements insertions

A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models

SNP genotyping in polyploids

Utilities for analyzing next generation sequencing data.

Estimation of per-individual inbreeding tracts under a probabilistic framework

Estimation of pairwise distances under a probabilistic framework

Genotype likelihood simulator for VCF/BCF files

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

Estimating temporally variable selection intensity from ancient DNA data with a combination of forward- and backward-in-time simulations

Estimating temporally variable selection intensity from ancient DNA data

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

A pipeline to impute plink genotypes to 1000 Genomes phase 1

Perl software to cluster SNPs based on its genotype.