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 structure alignment
 * Homology modeling by (iteratively) combining sequence and structure alignment data
 * 'Filtering' of Blast or other pairwise alignments
 * Combining many alignments into 1 consensus
 * Multiple genome alignment (can cope with rearrangements)