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).