HH-suite

HH-suite is a software tool designed for sensitive sequence searching and protein homology detection. It is particularly focused on finding homologous sequences in large databases using HMM-HMM (Hidden Markov Model - Hidden Markov Model) comparisons. HH-suite builds on the principles of HMMER and allows for the comparison of sequences to HMMs derived from multiple sequence alignments, enabling the identification of distant homologs that might not be detected by traditional sequence alignment methods.