MAFFT multiple sequence alignment software version 7: Improvements in performance and usability

Abstract

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations. © 2013 The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.