Figure 1.

Large-scale comparative evolutionary analysis procedure for conservative inference of positively selected genes and codons. (A) Orthology inference, multiple sequence alignment, and alignment filtering/masking steps. (B) Maximum likelihood evolutionary analyses, statistics and manual curation steps. Both stages were subject to rigorous curation and quality control at all steps. See main text and Methods for details. See Supplementary Figure S2 for detailed results of the various ML parameter combinations (B). See Figure 3 for a breakdown of the artefacts (B).