Figure 7From: MUSCLE: a multiple sequence alignment method with reduced time and space complexityAdditive profiles. The profile functions in MUSCLE require amino acid frequencies for each column. Here we show the alignment of two profiles X and Y, giving a new profile Z. Note that the count nZ i for amino acid i in a given column of Z is the sum of the counts in the child profiles, i.e. nZ i = nX i + nY i . In terms of frequencies, this becomes f Z i = NXf X i /NZ + NYf Y i /NZ, where NX, NY, NZ are the number of sequences in X, Y and Z respectively. Therefore, given a suitable sequence weighting scheme, it is possible to compute frequencies in Z from the frequencies in X and Y. This avoids the step of building an explicit multiple alignment for Z in order to compute frequencies, as done in CLUSTALW and MAFFT.Back to article page