pyelton/Synteny-based-annotator
This collection of scripts will provide annotations for hypothetical proteins and poorly-annotated prokaryotic genes. If you are a microbiologist with a newly sequenced genome, I highly recommend this script. The citation for the paper on the method development can be found here: Yelton, A.P., Thomas B.C., Simmons, S.L., Wilmes P., Zemla A., Thelen M.P., Justice N., Banfield J.F. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Computational Biology. In press.