Local Installation

You can either (a) download and install the web service locally or (b) download the command-line interface. Please click here in case you want to use our hosted service.


You will need the following things properly installed on your computer.

  • Java 8 or higher

Haplogrep works on Linux, macOS and Windows. Please note that fasta input files are currently supported for Linux and macOS only.

Download and Install

Linux or macOS

Download and install the latest version from our download page using the following commands:

wget https://github.com/genepi/haplogrep3/releases/download/v3.2.1/haplogrep3-3.2.1-linux.zip
unzip haplogrep3-3.2.1-linux.zip


Download the latest Windows version from our download page.

  • Open the zip file and extract it content to a folder of choice.

  • Open the PowerShell and navigate to your folder where you extracted the *.exe file.

You are now ready to use Haplogrep by running haplogrep.exe.

Run Haplogrep

The following command starts a web service locally:

./haplogrep3 server

In case you want to run Haplogrep on the command-line execute the following command:

./haplogrep3 classify


Click here to learn about all command-line parameters.