Phat - a Pretty Handy Annotation Tool
by Anthony Wirth, Simon Cawley and Terry Speed
Phat is a program for finding genes in eukaryotic organisms. It was originally developed with a view to annotating Plasmodium falciparum data but now comes with code to retrain it for other organisms. (Requires annotated Genbank files for input).
The latest version comes with ready-made parameter sets for the analysis of:
Phat supports most input sequence formats and has support for analyzing sequences in parallel if you have a multiple-processor machine. (Requires BioPerl)