Preliminary release of EvidentialGene/Gnodes 
is included in evigene21jul30.tar, as the major portion updated (and a year's genome data/soft engineering, tests)
Gnodes differs from popular Evigene-RNA tools, by bringing in genomic DNA as evidence.
Gnodes is a measuring tool for both chromosome assemblies and the genes there-in, and RNA-assembled genes.
One of its most useful aspects is a measure of gene-duplications that is fully evidence-based, resting
upon gDNA coverage depth analyses, for unique conserved, 1-copy genes, and then all the other genes, and 
remainder of genome (tranposons, repeats, etc).  

Please see http://eugenes.org/EvidentialGene/other/gnodes/ for summaries and details.