Mutation rate calculation

Hi @aitor.blancomiguez or any other strainphlan experts,

Is it possible to explain the details of how mutation rate is calculated when --mutation_rate is specified as an option? Any resource that explains this would also be helpful. Thank you!

Hi @Jeffrey_Chiu
Sorry for the late reply, I was out for my summer holidays.
For the mutation rates, StrainPhlAn will rely on the internal call of PhyloPhlAn for the calculation (Home · biobakery/phylophlan Wiki · GitHub). This is, after discarding markers and samples in the first step, the filtered set of markers and samples will be provided to PhyloPhlAn to infer the phylogeny. In this step, PhyloPhlAn will calculate the mutation rates as the number of bases that differ between each pair of samples (using the alignment of the filtered set of marker genes) divided by the number of positions shared (i.e. containing no gaps) between the samples.