Edwards RJ (2019): Phylogenetic Tree Rooting, In Encyclopedia of Bioinformatics and Computational Biology, Elsevier Volume 2, Pages 727-735. Science Direct
A phylogenetic tree is a graphical representation of the evolutionary relationships between biological entities, usually sequences or species. Relationships between entities are captured by the topology (branching order) and amount of evolutionary change (branch lengths) between nodes. The role of the root is to add direction to these relationships and clearly define ancestry. This chapter will discuss if, when and why a phylogenetic tree should be rooted. Common rooting methods (midpoint and outgroup rooting) are introduced with comments on when to use them and how to recognize them in published trees.