Easiest way to install HMMER is with your favorite packager for your system:

  % brew install hmmer               # OS/X, HomeBrew
  % port install hmmer               # OS/X, MacPorts
  % apt install hmmer                # Linux (Ubuntu, Debian...)
  % dnf install hmmer                # Linux (Fedora)
  % yum install hmmer                # Linux (older Fedora)
  % conda install -c biocore hmmer   # Anaconda

Thanks to all the people who do the packaging!

Or, brief instructions for obtaining and compiling source code:

  % wget http://eddylab.org/software/hmmer/hmmer.tar.gz
  % tar zxf hmmer.tar.gz
  % cd hmmer-3.4
  % ./configure --prefix /your/install/path
  % make
  % make check
  % make install
  % (cd easel; make install)

The make check is optional. It runs a test suite that checks for errors in the software.

The make install is optional too. It installs programs in /your/install/path/bin/ and manual pages in /your/install/path/share/man/man1. If you don't provide a --prefix to ./configure to specify the installation path, the default is /usr/local.

The (cd easel; make install) in Easel installs a set of other small tools and their man pages. We don't make this part of the HMMER make install because Easel is part of other packages (Infernal, for example) and you might have already installed Easel tools.

HMMER compiles and runs on any POSIX-compliant system with an ANSI C compiler, including Mac OS/X, Linux, and any UNIX operating systems, provided it supports SSE2, ARM NEON, or big-endian Altivec/VMX vector instructions. This includes essentially all Intel/AMD compatible machines, Apple OS/X Intel or ARM machines, and some PowerPC machines. For more installation and configuration options, see the Installation chapter of the User Guide.