As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on variation due to shared selective pressures. In comparative sequence analysis, for example, sequence similarity is often used to illuminate important regions of the genome, but if the comparison is between closely related species, then similarity is the rule rather than the interesting exception. Furthermore, and perhaps worse yet, the contribution of a divergent third species may be masked by the strong similarity between the other two. Here we propose a remedy that weighs the contribution of each species according to its phylogenetic placement.