Wheels are provided for Linux x86-64 platforms, but other machines will have to build the wheel from the source distribution. Building pyhmmer involves compiling HMMER3 and Easel, which requires a C compiler to be available.


pyhmmer is hosted on GitHub, but the easiest way to install it is to download the latest release from its PyPi repository. It will install all dependencies then install pyhmmer either from a wheel if one is available, or from source after compiling the Cython code :

$ pip install --user pyhmmer

EMBL Package Registry

You can also install manylinux wheels built from the latest commit that passed the unit tests. Those bleeding-edge releases are available in the GitLab Package Registry hosted on the EMBL git server. Just instruct pip to use an extra index URL as follow:

$ pip install --user pyhmmer --extra-index-url

GitHub + pip

If, for any reason, you prefer to download the library from GitHub, you can clone the repository and install the repository by running (with the admin rights):

$ pip install --user


Keep in mind this will install always try to install the latest commit, which may not even build, so consider using a versioned release instead.

GitHub + setuptools

If you do not want to use pip, you can still clone the repository and run the file manually, although you will need to install the build dependencies (mainly Cython):

$ git clone --recursive
$ cd pyhmmer
$ python build
# python install


Installing packages without pip is strongly discouraged, as they can only be uninstalled manually, and may damage your system.