hh-suite (spack): HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. 
Keywords: alignment|bioinformatics|cpp|hh-suite|hhblits|hhpred|hhsearch|opensource|profile-profile-search|profile-search|protein-structure|sequence-search|simd|viterbi