EBA (Evolutionary Breakpoints Analyser) is a Perl-based pipeline that automatically defines, classifies, and scores Evolutionary Breakpoint Regions (EBRs) from pairwise synteny data across multiple genomes. It operates at multiple resolutions simultaneously and uses a phylogenetic classification to assign breakpoints to evolutionary branches.

Usage: perl EBA.pl -n -d -r -p -t -c classification.eba -chr chr_size.txt -o -k

Note: GD/GDGraph visualizations are optional. The core analysis pipeline runs fully without them. Install perl-gd and perl-gdgraph separately if you need graphical output on a supported platform.