Several Tools for Genome Comparison

AGenDA - Alignment-based Gene Detection Algorithm

AggloIndel - Unraveling overlapping indels by agglomerative clustering

CEGeD - Calculate Evolutionary Genome Distances

CG-CAT - Comparative Genomics - Contig Arrangement Toolsuite

DCJ - UniMog is a software tool unifying five genome rearrangement distance models

FFGC - Family Free Genome Comparison (FFGC) is a self-contained workflow system that provides functionality for all steps of a family-free gene order analysis starting from annotated genome sequences.