Installing SeqAn

There are different ways to install SeqAn, we recommend to try these in the given order:

  1. Native package management of the operating system.
  2. Unpacking the library package from
  3. Using the full sources from our github repository.

If possible, use the first option. If SeqAn is not available for your operating system, or if it is outdated, use the second option.

Use the third option if you want to use the master or develop branch which might contain bug-fixes and new features.

Native package management

SeqAn is available natively on the following platforms.


Before you install, please make sure that the version supplied is not completely out of date (a difference of 0.1.* is okay, but if the difference is bigger use the Library Package below). The current version of SeqAn is always shown on the SeqAn-Homepage and the version available on your platform is usually displayed in the info-link below.

Operating System Package Name Command links
Arch seqan (AUR) depends info
Debian libseqan2-dev apt install libseqan2-dev info | contact
Fedora seqan2-headers yum install seqan2-headers info | contact
Gentoo seqan emerge sci-biology/seqan info | contact
Ubuntu libseqan2-dev apt install libseqan2-dev info | contact
Homebrew seqan brew install homebrew/science/seqan info | contact
MacPorts seqan port install seqan info | contact
FreeBSD seqan pkg install seqan info | contact
OpenBSD seqan pkg_add seqan info | contact

You should execute the above commands in a terminal as the root user or prefix them with sudo. If you have problems installing the package on your operating system, or it is outdated, please write to the contact shown above (and replace () in the e-mail-address with @).

Library Package

First you need to download the most recent “library package” from and extract its contents. Now copy the include and share folders to their target location. This could be one of the following:

  • /usr/local so they are available system-wide and automatically found by your program [requires root or sudo]
  • /opt/seqan available system-wide and easy to remove again [requires root or sudo]
  • ~/devel/seqan some place in your home directory [does not require root or sudo]

In any case it is important to remember where you installed it to.

Full Sources

Make sure that you have git installed. For the operating systems mentioned above it can usually be achieved by using the respective command with git as package name.

For Windows there is Git client and shell available here.

Next create the required folders and clone our master branch:

~ # mkdir -p ~/devel
~ # cd ~/devel
~ # git clone seqan

You can update this branch at a later point by running git pull in ~/devel/seqan .