Convergent evolution in coding sequences. (A) Distributions of log10(P-value) of Pelican tests for real Murinae_seq data (black; all sites and excluding constant sites), simulated negative controls (blue; 1/1000 quantile is indicated), simulated positive controls (red; number of transitions is indicated; dashed lines show the minimum P-value). (B) Scatterplot displaying log10(P-value) of Pelican tests for all sites common to Murinae_seq (x-axis) and Total_seq (y-axis). The density plot is in black. Blue and dashed red lines as in A for Murinae_seq and as in Supplemental Figure S20A for Total_seq. (C) Top 21 best sites found by Pelican with Murinae_seq data set. (D) Genes ordered according to Pelican's best site-wise P-value in the Murinae_seq data, with 1/1000 threshold in blue. DE genes indicated by triangles. Genes that belong to selected significant GO-term are indicated. Star indicates a significant enrichment (adjusted P-value < 0.1). (E) Same for Total_seq data.
