Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals

Using time-reversible Markov models is a very common practice in
phylogenetic analysis, because although we expect many of their
assumptions to be violated by empirical data, they provide high
computational efficiency. However, these models lack the ability to infer
the root placement of the estimated phylogeny. In order to compensate for
the inability of these models to root the tree, many researchers use
external information such as using outgroup taxa or additional assumptions
such as molecular-clocks. In this study, we investigate the utility of
non-reversible models to root empirical phylogenies and introduce a new
bootstrap measure, the rootstrap, which provides information on the
statistical support for any given root position. Availability and
implementation: rootstrap support is implemented in IQ-TREE 2 and a
tutorial is available at the iqtree webpage
http://www.iqtree.org/doc/Rootstrap. In addition, a python script is
available at https://github.com/suhanaser/Rootstrap