An improvement on iterative analysis and more stringent results.
On some of our internal genomes we have been evaluating, we have been noticing slight overlap on the annotation. Mainly, the start and stop codon may interfere slightly and cause cWGAP's program to report a gene that overlaps 1bp - which is most likely false (but hey, it is biology.) We implemented the overlap analysis to create more stringent results to prevent false positives from showing up, but, of course, this may cause real results to be filtered. This depends on a lot of what has been done to the genomes. Your mileage may vary.