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It is now common to survey microbial communities by sequencing nucleic acid material extracted in bulk from a given environment. Comparative methods are needed that indicate the extent to which two communities differ given data sets of this type. UniFrac, which gives a somewhat ad hoc phylogenetics-based distance between two communities, is one of the most commonly used tools for these analyses. We provide a foundation for such methods by establishing that, if we equate a metagenomic sample with its empirical distribution on a reference phylogenetic tree, then the weighted UniFrac distance between two samples is just the classical Kantorovich–Rubinstein, or earth mover’s, distance between the corresponding empirical distributions. We demonstrate that this Kantorovich–Rubinstein distance and extensions incorporating uncertainty in the sample locations can be written as a readily computable …