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.

Family-free methods for gene order analyses do not require prior knowledge of evolutionary relationships between the genes across the studied genomes. This tool features a complete workflow for genome comparison, requiring nothing but annotated genome sequences as input.

Surprisingly, the continuous development of family-free methods recently lead to an integrated method for inferring gene families across several species. FFGC now includes a subworkflow for inferring gene families simultaneously based on gene similarities and family-free genome rearrangements (OrthoFFGCʜ and OrthoFFGCʜ≈ extensions).

FFGC is available for download at our git repository (https://gitlab.ub.uni-bielefeld.de/gi/FFGC) or as a Conda package at Bioconda (https://anaconda.org/bioconda/ffgc).

In general, three major steps are performed: (1) the computation of local sequence alignment scores between genes of two or more gene order sequences using BLAST+ or Diamond; (2) the establishment of gene relationships; and (3) the actual family-free gene order analysis.

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