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

mapping pipeline for ancient DNA

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript.

Coprolite host Identification pipeline

The mitochondrial workbench

R Package - Spatiotemporal Ancestry Interpolation and Search

Ancient DNA Read Simulator for Metagenomic

Repository for data, code & figures related to the publication: "Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic"

🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Backend for all sidora applications

Estimation of natural selection and allele age from time series allele frequency data using a novel likelihood-based approach

Research compendium for ‘Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data’; If you want to perform spatio-temporal similary search with the mobest R package as presented in the paper, then you can directly check the documentation here: https://nevrome.de/mobest

A realistic-ish aDNA simulator

The Clip&Merge Method for paired end read merging and adapter clipping, quality trimming and other FastQ operations.

R Package - Handling .janno files in R

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

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations

Estimating temporally variable selection intensity from ancient DNA data

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