PhyloScan allows a p-value cutoff α, which defaults to 0.05, such that sites in a user-specified clade of interest that are worse than this cutoff are not permitted to be strengthened by data from the other species via the combination process. This feature allows the user to concentrate on a single clade or species rather than the entire tree of species. Because of this cutoff, it is appropriate to modify the above formula for sites that survive the cutoff: