Repository of code for the paper "The evolutionary history of Neandertal and Denisovan Y chromosomes" by Petr et al.

R Package - Handling .janno files in R

Phylogenetic intersection analysis (PIA) from the Allaby lab, University of Warwick: doi.org/10.3389/fevo.2020.00084

Statement of the Ethics Discussion Group at the Department of Archaeogenetics (MPI-SHH/MPI-EVA)

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods

An ancient DNA genetic relatedness estimation software relying on pedigree simulations

Burrow-Wheeler Aligner for short-read alignment (optimized for aeDNA)

Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog

Experiments with the genotype data generators in xerxes

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

R Package - Spatiotemporal Ancestry Interpolation and Search

Additional tools for manipulating PIA output.

grups.plots is a companion R package to grups-rs, providing with a Shiny dashboard, harboring multiple interactive visualizations, utilities and summary statistics to analyse its results

A realistic-ish aDNA simulator

The Poseidon AADR Archive (PAA)

Program to generate RAxML sliding window trees

From .bam to .csv with annotated Y-chromosome variants

A CLI tool to run SQL queries on Poseidon .janno files

Website and data repository a directory of ancient metagenomic labs

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