Ambiguities in sequences
By default, MicrobeTrace averages ambiguities i.e. it averages any possible resolutions. However, you can select the following options from a drop down menu. Once you choose this option, it will become your default setting for future sessions.
-resolve (count any resolutions that match as a perfect match)
-average (average all possible resolutions)
-skip (skip all positions with ambiguities)
-GapMM (count character-gap positions as 4-way mismatches, otherwise same as average)
-HIV-Trace-g (Any sequence with no more than the selected proportion [0 - 1] will have its ambiguities resolved [if possible], and ambiguities in sequences with higher fractions of them will be averaged. This mitigates spurious linkages due to highly ambiguous sequences.)