HMMER Altivec optimizations
Macintosh PowerPC's running OS/X will see about an eight-fold increase, thanks to Altivec optimizations contributed by Erik Lindahl at Stanford.
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly moreaccurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
As part of this evolution in the HMMER software, we are committed to making the software available to as many scientists as possible. Earlier releases of HMMER were restricted to command line use.