Count number of substitutions in each direction for amino acids pairs. AsymmetryCounter can test protein sequence data for substitutional asymmetry using the technique described in McDonald et al. (1999). Under the neutral model of protein evolution, a comparison of sequences from two species should show equal numbers of substitutions in each direction for each pair of amino acids. For example, when comparing the mesophile (moderate habitat temperature) Bacillus subtilis with the thermophile (high habitat temperature) Geobacillus stearothermophilus, you would expect the number of sites with alanine in B. subtilis and proline in G. stearothermophilus to equal the number of sites with proline in B. subtilis and alanine in G. stearothermophilus. In fact, a data set of 229 proteins showed 122 aligned sites with the first pattern and only 69 sites with the second pattern, suggesting that proline is preferred by natural selection over alanine in G. stearothermophilus (McDonald et al. 1999).

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