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Alignment time for Clustal Omega (red), MAFFT (blue), MUSCLE (green) and Kalign (purple) against the number of sequences of HomFam test sets. Average sequence length is rendered by point size. Both axes have logarithmic scales. Clustal Omega and Kalign were run with default flags over the entire range. MUSCLE was run with –maxiters 2 for N>3000 sequences. MAFFT was run with --parttree for N>10 000 sequences.
