HMMER
HMMER is a bioinformatics software package for sequence analysis that uses profile hidden Markov models (HMMs) to detect homologous sequences and conserved domains. It was developed by Sean R. Eddy and is widely used in protein family annotation and genome analysis. The current major release, HMMER3, emphasizes speed and sensitivity for large-scale data sets and is distributed as open-source software.
Core tools in the HMMER suite include hmmbuild, which constructs a profile HMM from a multiple sequence
HMMER reports sequence similarity using log-odds scores, E-values, and bit scores; search results include alignments and
History and availability: HMMER originated in the mid-1990s, with HMMER3 released in the early 2010s as a