HMMER [1] is a well-known bioinformatics tool/software. It offers a web server and a command-line tool for users. Here are some additional applications of HMMER.

HMMER is most widely used for sequence analysis. It is based on profile Hidden Markov Models (HMMs). HMMER command-line consists of various modules that are used for different tasks. Besides multiple sequence alignment (MSA), HMMER can be used for some other tasks in bioinformatics. Its uses and applications are mentioned below.

• Homology search can be easily performed using HMMER. If you are working with protein sequences then use PHMMER.
• build a local database of your own and then perform a homology search within it using a query sequence.
• add column masks to MSAs using the alimask module.
• align sequences to a profile.
• construct profiles from MSAs.
• convert profile files to various formats.
• retrieve profiles from a file.
• generate a conversation logo from a profile.
• search sequences against a profile and sequence database.
• search DNA/protein queries against profile and sequence database.
• You can also perform a homology search iteratively.
• translate DNA into 6 frames.
• calculate sequence weights in MSAs.
• mask sequence residues.
• in addition to the creation of consensus secondary structures, you can also calculate the accuracy of predicted RNA secondary structures using HMMER.
• reverse compliment an MSA.
• map two alignments to each other.

These are only a few tasks that you can perform using the HMMER web server and command-line tool. HMMER command-line tool performs more tasks than mentioned here. For more details, read its documentation.

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References

1. https://www.ebi.ac.uk/Tools/hmmer/