Data analysis tools and pipelines

Many tools, programs, pipelines, and software suites are used in the analysis of ancient biomolecules. Below are a collection of commonly used software resources, including with links for their download. If you have add additional resources to suggest, please send your suggestions to

Ancient DNA

Multipurpose GUI platforms

Initial data handling and quality assessment

DNA sequence alignment

DNA sequence assembly

Ancient DNA damage

Variant calling and genotyping

Sex, kinship, and contamination

Ancestry and admixture


Population and evolutionary history

Species identification and metagenomics

Visualization tools

Ancient Proteins

Stable Isotopes