HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

[hmmer-3.0a1.tar.gz] Archive of stable representatives of the HMMER1 and HMMER2 lineages The 1992-1998 HMMER1 lineage was closer to the original Krogh/Haussler conception of profile HMMs.

We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems, provided it supports SSE2, ARM NEON, or big-endian Altivec/VMX vector instructions.

Publications from the HMMER project