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: (1) the computation of local sequence alignment scores between genes of two or more gene order sequences using on BLAST+ (Necessary BLAST+ binaries are included in the binary releases of this software); (2) the establishment of gene relationships; and (3) the actual family free gene order analysis.