SAM HMMER format file
File type: Various data file
A .hmmer file contains a profile hidden Markov model in HMMER format for the Sequence Alignment and Modeling system (SAM).
SAM uses the model to represent sequence patterns and perform sequence analysis.
File type category:
Various data file
Date updated: September 28, 2026
The SAM HMMER format is a text-based format for storing profile hidden Markov model data. A profile HMM describes the conserved and variable positions in a family of biological sequences.
The format belongs to the Sequence Alignment and Modeling system, which uses hidden Markov models for sequence alignment and modeling. The file is one of the model-data files used by SAM.
SAM is designed for Linux and Unix systems. A HMMER file can also be inspected as text, but its model data should be handled with software that understands the SAM HMMER format.
Open the file with the Sequence Alignment and Modeling system on Linux or Unix. Use the SAM tools that read HMMER-format models for sequence analysis.
Because the format is text-based, a plain-text editor can display its contents, but editing the model manually may make it unusable to SAM.
A .hmmer file is normally used directly as a SAM model file and does not need conversion. If a different model format is required, use a SAM utility that explicitly supports importing or exporting the relevant format.
Do not rename the file as a way of converting it; changing the extension does not change the model data.
Software applications that can open hmmer files:
Linux/Unix
Software applications that can edit hmmer files:
Linux/Unix
Software capable of saving hmmer files:
Linux/Unix
Software apps that create hmmer files:
Linux/Unix
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