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Pseudofinder

Automated detection of pseudogene candidates in prokaryotic genomes.

Pseudofinder is a bioinformatics tool that detects pseudogene candidates from annotated genbank files of bacterial and archaeal genomes.

It has been tested mostly on genbank (.gbf/.gbk) files annotated by Prokka with the --compliant flag (i.e. including both /gene and /CDS annotations).

There are alternative programs for pseudogene finding and annotation (e.g. the NCBI Prokaryotic Genome Annotation Pipeline), but to the best of our knowledge, none of them are open source or allow easy fine-tuning of parameters.

Citing Pseudofinder

Pseudofinder is developed by Mitch Syberg-Olsen¹, Arkadiy Garber², Patrick Keeling¹, John McCutcheon², and Filip Husnik³.

¹ University of British Columbia, Vancouver, Canada

² Arizona State University, Tempe, Arizona, USA

³ Okinawa Institute of Science and Technology, Okinawa, Japan

If it was useful for your work, please cite it as:

Syberg-Olsen MJ*, Graber AI*, Keeling PJ, McCutcheon JP, Husnik F. Pseudofinder: detection of pseudogenes in prokaryotic genomes, Molecular Biology and Evolution 2022, 39(7): msac153, doi: https://doi.org/10.1093/molbev/msac153.

*Co-first authors.

Please also cite various dependencies used by Pseudofinder.