Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.

Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the best alignment according to manual inspection by human experts is found. Ideally, this should be assisted by an automatic assessment of the alignment quality. Our web-site http://msa.cgb.ki.se allows users to perform all these steps: Kalign to align sequences, Kalignvu to view and verify the resulting alignments and Mumsa to assess the quality. Due to the computational efficiency of Kalign we can allow users to submit hundreds of sequences to be aligned and still guarantee fast response times. All servers are freely accessible and the underlying software can be freely downloaded for local use.