See hmmer.org to download release tarballs and documentation, or just download the source tarball for the current version, HMMER 3.4, from this link.
Our git repo is only for managing the development team. Although the head of the master branch always corresponds to the most recent HMMER release, our release tarballs include other things you need to build and use HMMER, including our Easel library and prepackaged PDF documentation.
You probably don't want to download from the autogenerated github "Assets" links below unless you're a developer and you know what you're doing.