Phylogenetic and population genetic methods for detecting positive selection serve as complementary tools for functional and evolutionary analysis. These methods operate at different time scales, with phylogenetic methods being best suited for detecting selection that operates over relatively long periods in evolutionary history, and population genetic methods being best suited for detecting more recent selection. Population genetic methods can potentially detect selection operating at individual sites, through the effects of linkage with flanking alleles, while phylogenetic methods generally require multiple sites to have been affected in a sequence of interest. At the same time, decay of linkage disequilibrium at longer evolutionary time scales can allow phylogenetic methods to more accurately pinpoint the specific locations of functionally important substitutions. In some cases, phylogenetic methods also allow such substitutions to be mapped to particular branches of a phylogenetic tree, thereby providing useful insights about the evolutionary histories of the sequences in question.