Summary: We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably effective. We also conclude that for a web server with moderate usage (10K hits/month) the cloud provides a cost-effective alternative to in-house deployment.Centro de Regulación Genómica (CRG to C.N., P.T., C.K.); Plan Nacional (BFU2008-00419); Lleida University, the Spanish ministry of education (TIN2008-05913 to M.O., F.G., F.C.); the Consolider Project (CSD 2007-00050); Super-computacion y e-Cienia (SYEC).