question: Identifying the root of a phylogenetic tree is important because incorrectly rooted phylogenetic trees may mislead evolutionary and taxonomic inferences. Many techniques for inferring the root have been proposed, but each has shortcomings that may make it inappropriate for any particular dataset. Here we outline the various ways to root phylogenetic trees, which include: outgroup, midpoint rooting, molecular clock rooting, and Bayesian molecular clock rooting. In addition, we discuss the pros and cons and also list software availability for each of the rooting methods.