PLINK (opens new window) is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Install PLINK 1 (opens new window) with the following command:

sudo apt install plink

And use the following executable:

plink1 --noweb

Install PLINK 1.9 (opens new window) with the following commands:

sudo apt install plink1.9

And use the following executable:


You can also install PLINK 1.9 with Bioconda. See our Anaconda and Bioconda tutorial for more details.

Installing PLINK 2 (opens new window) is a little more cumbersome as it is not available in Ubuntu's package repositories.

You can either use Conda (opens new window) to install Plink2 package (opens new window) or follow with binary release below.

To install package into your Conda (opens new window) environment use this command:

conda install -c bioconda plink2

To download and unpack the binary for PLINK 2 follow these steps:

# Create a local binary directory in your home directory
mkdir ~/bin

# Download the latest binary of PLINK 2.
wget -P ~/bin/ http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip

# Install unzip
sudo apt install unzip

# Unzip the archive
unzip ~/bin/plink2_linux_x86_64_latest.zip -d ~/bin/

# Remove archive
rm ~/bin/plink2_linux_x86_64_latest.zip

You can now use the following executable: