Figure 6.

Ortholuge R1 × R2 plots for the prokaryotic data, illustrating two ortholog data sets and a true-negative data set. (A) Putative orthologous groups from an RBH-predicted data set. (B) Probable true orthologs from a higher quality (more precise) data set. (C) True-negative orthologs (i.e. true paralogs) from the "gene-loss simulation" data set. Darker dots represent putative orthologous groups which have had an ingroup1 true-negative (paralog) introduced into the group. Lighter dots represent putative orthologous groups which have had an ingroup2 true-negative (paralog) introduced into the group. (D), (E), (F) are zoomed-in versions of (A), (B), (C), respectively, with axes shown from 0 to 2 instead of 0 to 10. Most putative ortholog groups (particularly for the high quality data set) exhibit low Ratio1 and Ratio2 values (for example, all values are less than 1 for the points in the high quality data set plot), whereas most true-negative groups exhibit higher Ratio1 and Ratio2 values (i.e. only 9% of ingroup1 true negative introductions, and 6% of ingroup2 true negative introductions, have points with Ratio1 and Ratio2 values less than 1).