Figure 2. Individual sites of the vertebrate rhodopsin alignment used to illustrate similarities and differences between FEL and MEME.

Branches that have experienced substitutions, based on most likely joint maximum likelihood ancestral reconstructions at a given site, are labeled as count of synonymous substitutions:count of non-synonymous substitutions. The thickness of each branch is proportional to the minimal number of single nucleotide substitutions mapped to the branch. Branches are colored according to the magnitude of the empirical Bayes factor (EBF) for the event of positive selection: red – evidence for positive selection, teal – evidence for neutral evolution or negative selection, black –Ê no information. See Methods for more detail. All three sites were identified as experiencing positive diversifying selection by MEME. FEL reported site 54 as positively selected, site 273 as neutral, and site 210 as negatively selected.