Align-m

Align-m is a multiple sequence alignment program written by Ivo Van Walle.

Align-m has the ability to accomplish the following tasks:
 * multiple sequence alignment,
 * include extra information to guide the sequence alignment,
 * multiple structural alignment,
 * homology modeling by (iteratively) combining sequence and structure alignment data,
 * 'filtering' of BLAST or other pairwise alignments,
 * combining many alignments into one consensus sequence,
 * multiple genome alignment (can cope with rearrangements).