Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. The main use case is through SingleM, although it can be used independently without issue to search and cluster other pre-aligned sequences.

Smafa can be installed in the usual way Rust packages are installed. After installing Rust, smafa can be installed using cargo:

cargo install smafa

To run the aligner, first make a db with smafa makedb and then query that database with smafa query. To see how to use these modes, use e.g. smafa query --help.

If you have any questions or comments, please raise an issue on the GitHub repository, or just email Ben Woodcroft.

Smafa is developed by the Woodcroft lab at the Centre for Microbiome Research, School of Biomedical Sciences, QUT. It is licensed under GPL3 or later.

The code is available at https://github.com/wwood/smafa.