Figure 7.

Additive 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 n^Z_i for amino acid i in a given column of Z is the sum of the counts in the child profiles, i.e. n^Z_i = n^X_i + n^Y_i. In terms of frequencies, this becomes f ^Z_i = N^Xf ^X_i /N^Z + N^Yf ^Y_i/N^Z, where N^X, N^Y, N^Z 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.