Robust Inferences from Ambiguous Alignments
Benjamin D. Redeling, Marc A. Suchard · 2009
This chapter discusses several traditional methods of handling ambiguity in multiple sequence alignments, as well as new statistical approaches to this problem, and describes how alignment uncertainty can affect phylogeny estimation by focusing on a small data example. This example demonstrates the negative effects of ignoring alignment uncertainty and illustrates the practical benefits of the new statistical methods.