Aegean

• canon-gff3(1) create canonical GFF3
• gaeval(1) calculate coverage and intergrity scores for gene models based on transcript alignments
• locuspocus(1) calculate locus coordinates for the given gene annotation
• parseval(1) comparative analysis of two alternative sources of annotation
• pmrna(1) filter out all but the primary isoform from each gene of the input
• tidygff3(1) tidy GFF3 file
• xtractore(1) extract sequences corresponding to annotated features from the given sequence file