RootDigger: a root placement program for phylogenetic trees

Abstract

AbstractSummaryIn phylogenetic analysis, it is common to infer unrooted trees. Thus, it is unknown which node is the most recent common ancestor of all the taxa in the phylogeny. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as midpoint rooting or rooting the tree at an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. We present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement.Availability and implementationRootDigger is available under the MIT licence at https://github.com/computations/root_digger