The final HMMER3 beta test release is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your $PATH if you like. If the precompiled versions don’t work for you, you can always compile your own version from the source.
The main additions in 3.0b3 are parallelizations and even more speed. It now includes support for multicores (POSIX multithreading) and support for clusters (MPI). For the first time, we’re seeing some searches peek above NCBI BLAST search speed. Yes, you read that right, profile HMM speeds have started to exceed BLAST speed. And we’re far from done.
The release notes for 3.0b3 follow: Continue reading →