euka (part of vgan) is a tool for bilaterian abundance estimation of ancient environmental DNA.

Haplocart (part of vgan) classifies modern human mtDNA haplogroup.

cinch is a non-negative matrix factorization tool to infer levels of tumor DNA from cell-free DNA.

ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity. ROHan can work on modern and ancient samples with signs of ancient DNA damage.

gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.

glactools is a set of command-line tools for the management of Genotype Likelihood (GL) and Allele Counts (AC).

DICE is a Bayesian method to jointly estimate error rates, demographic parameters and the rate of contamination from present-day humans in ancient DNA (aDNA) samples from modern or archaic humans. Our approach is based on an MCMC sampler, and is applicable to nuclear autosomal aDNA data. It can also serve to infer the most probable ancestry of the individual(s) that contaminated the sample.

schmutzi is a set of programs aimed at ancient DNA data that can estimate contamination based on deamination patterns alone, call a mitochondrial consensus for the endogenous genome while taking into account contamination and deamination and estimate mitochondrial contamination and identify the most likely contaminant.

deML is a program for maximum likelihood demultiplexing of next-generation sequencing data.

leeHom is a program to trim adapters and merge overlapping sequencing using a Bayesian reconstruction. This is particularly useful for ancient DNA and or DNA with a short fragment size like cell-free DNA.

Three-week graduate-level course on introduction to next-generation sequencing (NGS) data analysis, introduction to UNIX and command-line use.

Three-month graduate-level course to understand basic concepts in population genetics concepts and their links to human health and disease (starting Fall 2024)