ParsEval is a program for comparing two sets of gene structure annotations (provided as GFF3 files) for the same genomic region. Comparison statistics are calculated for each genic region, as well as for the entire region overall.
The Brendel Group @ Indiana University
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Standage, D.S. & Brendel, V.P. (2011)
ParsEval: parallel comparison and analysis of gene structure annotations
BMC Bioinformatics 2012, 13:187