HMMER data
File type: Various data file
Files with the .hmm file extension contain profile hidden Markov model data used by HMMER.
HMMER is a bioinformatics software suite for searching sequence databases for homologous protein sequences and analyzing protein sequence relationships.
File type category:
Various data file
Date updated: October 12, 2026
Record marked as obsolete and not updated for a long time.
HMMER is a command-line bioinformatics suite used to search sequence databases for homologous protein sequences and to build or use protein sequence alignments. An .hmm file normally contains one or more profile hidden Markov models built from sequence alignments.
The file is a text-based data file containing model parameters, including the probabilities used to represent conserved and variable positions in a sequence family. HMMER programs use these models as input for sequence searches and related analyses; they are not normally standalone documents.
HMMER is primarily used on Linux and other Unix-like systems. The .hmm format is considered obsolete, and older files may require conversion or a compatible HMMER release before they can be used reliably.
An .hmm file should be opened with the HMMER command-line tools that produced it or that are compatible with its format. Programs such as hmmsearch and hmmscan use profile HMM files for sequence searches, while hmmpress prepares a file for use as an HMM database.
The file can also be viewed as plain text in a text editor, but a text editor will not perform HMMER searches or interpret the model.
There is no general document conversion for HMMER data. The HMMER utility hmmconvert can convert compatible profile HMM files between supported HMMER formats.
If conversion is not possible, the usual alternative is to obtain the original sequence alignment and rebuild the profile with HMMER's hmmbuild program.
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