Clustal V: Multiple Alignment of DNA and Protein Sequences

CLUSTAL is a package for performing fast and reliable automatic multiple alignment of many DNA or protein sequences. It was originally written for IBM-compatible microcomputers (1,2) and was later reorganized as a single program for VAX mainframes. Recently (3), the package was completely rewritten as a new program, CLUSTAL V, which is freely available for a wide variety of computer systems and which has a number of new features. The main improvements are the calculation of phylogenetic trees from sequence data sets with a bootstrap option for calculating confidence intervals on the groupings and the ability to align alignments with each other.