Focus on a target species or clade
In running PhyloScan, the user must specify two cutoff values, and can optionally specify additional parameters describing the expected multiplicity of binding sites upstream of a regulated gene. The first cutoff is a p-value cutoff, calculated on a per intergenic-sequence basis for the clade that includes the species of primary interest. We chose a default value of 0.05, so that weak intergenic regions in the target species' clade will not be considered, even when strong intergenic regions are located in orthologous regions in more-distantly related species. The choice of a larger value would reduce the focus on the target species, allowing strong sites in other species to rescue weak sites in the target species. The choice of a smaller value would increase the focus on the target species; the choice of a very small value would effectively cancel out the information available from the related species, since any intergenic region that looks extremely promising in the target species will almost surely continue to look promising when additional data are included.