DNA sequence analysis made easy. AmbiguityRemover 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.

The programs available here require a set of aligned homologous pairs of protein sequences from two species. The AmbiguityRemover program takes the file of sequences and puts ambiguously aligned sites next to alignment gaps in lower case, so they can be ignored by the AsymmetryCounter program. AsymmetryCounter counts the number of substitutions in each direction for each pair of amino acids, and compares the ratio to the expected 1:1 ratio using a test of goodness-of-fit. AsymmetryScaler finds an asymmetry index that illustrates how preferred or unpreferred each amino acid is in one species.

The license of this software is Freeware, you can free download and free use this calculator software.