Brief installation instructions 
HMMER 3.1b2; February 2015
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These are quick installation instructions. For complete documentation,
including customization and troubleshooting, please see the
Installation chapter in the HMMER User's Guide (Userguide.pdf).

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Starting from a distribution "with binaries", such as 
hmmer-3.1b2-linux-intel-x86_64.tar.gz:
 uncompress:                uncompress hmmer-3.1b2-xyz.tar.gz  
 unpack:                    tar xf hmmer-3.1b2-xyz.tar
 move into new directory:   cd hmmer-3.1b2-xyz
 
The pre-compiled binaries are found in the directory ./binaries.
You may copy these into a directory of your choosing, or simply add
this directory to your $PATH variable.

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Starting from a source distribution, hmmer-3.1b2.tar.gz:
 uncompress:                uncompress hmmer-3.1b2.tar.gz  
 unpack:                    tar xf hmmer-3.1b2.tar
 move into new directory:   cd hmmer-3.1b2
 configure:                 ./configure
 build:                     make
 automated tests:           make check
 automated install:         make install

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HMMER is developed primarily on Linux and Mac OS/X systems. It is
tested on a variety of UNIX and UNIX-like operating systems. It is
written in ANSI C99 conforming to POSIX standards. It is meant to be
portable to any POSIX-compliant system with an ANSI C99 compiler,
including all UNIX and Macintosh systems. A binary version is also
available for Windows systems with Cygwin installed (Cygwin is 
optional POSIX compatibility software).

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Starting from a Subversion (SVN) working copy:

If you have checked HMMER out from its Subversion repository, there's
some additional stuff you need to do one-time-only in your new working
directory:

   ln -s easel/aclocal.m4 aclocal.m4
   autoconf
   (cd easel; autoconf)

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The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/