Comparative performance of MEME and FEL on 16 empirical alignments (see Results and Text S1 for an extended discussion of each individual case).

() reports the number of sequences (codons) in the alignment. () refers sites found by MEME to be positively (negatively) selected (). () denote sites found by FEL to be positively (negatively) selected (). references sites that are classified as neutrally evolving by FEL. Values in parentheses for the column show the mean p-values for FEL and MEME on this set of sites, respectively. Values reported in the rightmost column count the number of sites where MEME fits significantly better than FEL, based on a 2-degrees of freedom LRT (). Abbreviations: IAV = Influenza A virus, JEV = Japanese encephalitis virus.