Figure 3. New methods for analyzing evolution by recombination.

Improved models and visualization tools are needed to analyze recombination. Virulence genes, here exemplified by the acfD gene in the Vibrio cholerae pathogenicity island [43], often display complex recombination patterns. The aligned acfD genes (arrows) from three V. cholerae strains (M2140, M1567, and M1118) are plotted separately; a line connects each site where the nucleotides in two strains differ from the third strain. Noninformative sites were removed before plotting.