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Clustal Omega 1.2.4_1
If given already aligned sequences, by default Clustal Omega use the existing alignment to guide creation of the new alignment, by constructing a HMM from the existing alignment. Check this box to realign aligned sequences from scratch.
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.

References to cite