title: A reality check for alignments and trees.
abstract: Making multiple sequence alignments is one of the more commonplace procedures in modern biology. Multiple alignments are typically generated by feeding sequences into the alignment program from the N-terminus to the C-terminus. Recent results show that if the same sequences are processed from the C- to the N-terminus, a different alignment is often obtained. Because phylogenetic trees are built from alignments, the resulting trees can also differ. The new findings highlight sequence alignment as a crucial step in molecular evolutionary studies and provide straightforward measures to assess alignment reliability.
authors.affiliation: Institute of Botany III, University of Düsseldorf, Düsseldorf, Germany. w.martin@uni-duesseldorf.de
authors.forename: William
authors.initials: W
authors.lastname: Martin
authors.forename: Mayo
authors.initials: M
authors.lastname: Roettger
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Lockhart
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein