Our Scalable HMMer paper

Is available if you would like some good reading from IEEE.
For those who don’t know, we reworked the p7Viterbi function in the HMMer code, and created a faster version of HMMer in the process. Our measurements put it anywhere from 1.6-2.5x faster than the downloadable binaries from Professor Eddy’s site. Since HMMer is GPLed, our patch and binaries are available under that license from our download site.
If you wish to distribute binaries that are not covered by GPL or are unwilling to use the GPL for your product and want to distribute this code, please contact us.