Threshold consensus methods for molecular sequences

We introduce a parameterized threshold consensus method (th chi) for molecular sequences which is based on a majority-rule voting principle. In contrast to other frequency-based methods, the th chi method uses a single criterion to return ambiguity codes of different lengths. We derive basic features of the method and establish that it returns at most two ambiguity codes at any position of the consensus sequence. We bound from below the size of the frequency gap that exists when the th chi method returns an ambiguity code. Using such properties, we compare the th chi method to other consensus methods for molecular sequences which are defined in terms of threshold or gap criteria.