I have one concluding favor, to request of my Reader; that he will not expect to be equally diverted and informed by every Line, or every Page of this Discourse, but give some Allowance to the Author's Spleen, and short Fits or Intervals of Dullness...
Jonathan Swift, A Tale of the Tub
It includes a User Guide with introductory notes about installation and tutorial examples of command line usage. The guide is telegraphic, documenting basic usage of the new HMMER3 programs. It does not yet go into all the command line options -- partly because a few of them don't work as advertised yet.
Linux binaries are included, as well as source code. If you compile it for yourself, be aware that you need a compiler that deals well with Intel Streaming SIMD Extensions (SSE), specifically SSE2 code. The GNU C compiler gcc will compile HMMER fine, but it produces binaries with markedly suboptimal speed performance. We now use the Intel C compiler, icc, for production code. The Linux binaries in the tarball have been compiled with icc.
The purpose of the alpha test period is in part to smoke out any remaining bugs, of course, but also to give people a chance to give feedback on how it all behaves at the command line. The core of H3's functionality seems stable to me, but all the stuff that you see -- the applications, the command line options, the i/o formats -- is deliberately still protoypical and fluid. The invited alpha testers are a group of power users at centers that do high throughput annotation. In the test phase, I'd like to be free to make changes that make HMMER3 work best in anyone's analysis pipeline. The corollary to this is that you can't count on HMMER3 output formats just yet, so don't go writing any heavy duty parsers.
There are eleven "invited" alpha testers, but anyone else adventurous enough to test the code is welcome to. The code is publicly accessible. The best place to leave comments and discuss issues/problems/bugs is here at Cryptogenomicon.