Installation and Usage

Haplogrep is tree-independent and provides a plugin system to connect different phylogenetic trees with the software.

Install Trees

Haplogrep includes 3 trees (Phylotree 17 rCRS and RSRS, Phylotree Forensic Update) by default. To install one of our other available trees, enter the following command:

./haplogrep3 install-tree phylotree-rcrs@16.0

Please have a list of all available trees and commands to install them.

Tree Structure

All trees are publicly available on GitHub and consists of the following files:

  • A makefile to build the latest version automatically.
  • A YAML file including all required metadata (e.g. name, URL, last update) and links to the required files (e.g. phylogenetic tree, nomenclature rules, hotspots)
  • All files linked in the YAML file. The repository includes the phylogentic tree in XML format, the mutations weights, nomenclature rules and the amino acid changes files.
  • Required reference files for FASTA alignment. For each reference in fasta format, the files generated by bwa index are required. Additionally, a *dict file is required.

Please have a look at the Phylotree 17 rCRS repository to see the definition of a tree.

Add trees

You can integrate your own trees, by setting up a repository similar to this one and add the following command:

./haplogrep3 install-tree phylotree-rcrs-15/blob/main/src/tree.yaml

Share trees

To share trees, you can either add the tree to our meta repository or set up your own repository. To set up your own repository, adapt the haplogrep3.yaml file as follows:


This setup would then allow you to install trees like this:

./haplogrep3 install-tree my-new-tree@1.0