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Clustal Omega

By default, only a fraction of the distance matrix is calculated, for speed. Calculate full matrix may be more accurate under some circumstances but is slower and needs more memory.

Redo the alignment multiple times to improve accuracy. Both the HMM and the guide tree will be recalculated each time.

Normally, if iteration is specified, a new guide tree and HMM will be calculated for each iteration. Use this option to restrict the number of iterations for either.


  • Sievers, F. and Wilm, A. and Dineen, D. and Gibson, T. J. and Karplus, K. and Li, W. and Lopez, R. and McWilliam, H. and Remmert, M. and Soding, J. and et al.(2014). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega . Molecular Systems Biology doi