DO1:10.1080/10635150701294741 Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?

Abstract.—The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple align-ment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new ap-proach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available fro