Performance of AGEnt compared to other predictors of P. aeruginosa accessory genome. AGEnt was compared to IslandViewer, Panseq, and RGPs for identification of accessory genome sequences. (A) Colored bars represent the proportion of accessory genome coding sequences (CDS) identified by both AGEnt and the comparator method (red), identified by AGEnt but not the comparator method (purple), or identified by the respective comparator method but not AGEnt (green). (B) Evaluation of the accuracy of accessory genome identification by AGEnt and the comparator methods using gene homology searches as a gold-standard. Genes were considered homologous if they shared at least 50% sequence identity across at least 50% of the gene length. CDSs in each of the genomes were classified as accessory if they were found to have homologs in <90% of the twelve reference genomes by sequential sequence alignments (see Methods for details). Bars represent average percentage of total CDS called by each method as accessory (grey bars) or core (white bars) subsequently identified as accessory by gene homology.