BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection.

Inferring the selective forces that orthologous genes underwent across different lineages can help us understand the evolutionary processes that have shaped their extant diversity and the phenotypes they underlie. The most widespread metric to estimate the selection regimes of coding genes-across sites and phylogenies-is the ratio of nonsynonymous to synonymous substitutions (d/d, also known as ). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of orthologous genes across large numbers of species.