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Clustal Omega is currently under peer review. Please contact the developers/authors before citing Clustal Omega:

Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega
Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins