Practical multiple Sequence alignment

Abstract Multiple sequence alignment as a means of comparing DNA, RNA or amino acid sequences is an essential precondition for various analyses, including structure prediction, modeling binding sites, phylogeny or function prediction. This range of applications implies a demand for versatile, flexible and specialized meth- ods to compute accurate alignments. This chapter summarizes the key algorithmic insights gained in the past years to facilitate both, an easy understanding of the current multiple sequence alignment literature and to enable the readers to use and apply current tools in their own everyday research