SIMD-vectorized implementation of the Viterbi algorithm for profile HMM
alignment and introduced various other speed-ups. This accelerated HHsearch by a
factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is
~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch
and HHblits searches with many query profile HMMs can be parallelized over cores
and over servers in a cluster using OpenMP and message passing interface (MPI).