Wheels are provided for Linux and OSX 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


Pronto is also available as a recipe in the bioconda channel. To install, simply use the conda installer:

$ conda install -c bioconda pyhmmer

Arch User Repository

A package recipe for Arch Linux can be found in the Arch User Repository under the name python-pyhmmer. It will always match the latest release from PyPI.

Steps to install on ArchLinux depend on your AUR helper (yaourt, aura, yay, etc.). For aura, you’ll need to run:

$ aura -A python-pyhmmer

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.