UNIT 3.8 Computing Multiple Sequence/Structure Alignments with the T-Coffee Package

Abstract

In this unit, we describe assembly of a multiple sequence alignment using the T-Coffee package. T-Coffee is much more flexible than most related methods (e.g., ClustalW) because it makes it possible to combine many alternative alignments into a single one, based on an estimate of consistency between these alignments. This strategy can be especially useful when one has to decide among the output produced by several alternative methods. Curr. Protoc. Bioinform. 29:3.8.1-3.8.25. © 2010 by John Wiley & Sons, Inc.