Our research currently focuses mainly on multiple alignment of protein sequences and structures. Align-m aligns N sequences, using a truly multiple approach. It was shown to outperform T-Coffee, DiAlign and ClustalW on a large benchmark, SABmark, that covers the entire known fold space. In contrast, it runs about twice as slow as T-Coffee.

Align-m is also suitable for multiple structure alignment, and in general for combining alignments from various sources into 1 consensus. It can be forced to allow alignments that are not colinear, so that e.g. proteins with a circular permutation, or genomes with rearrangements, can be correctly aligned.