Ways to determine Statistics for a simulation #5
Description
Greetings,
I have an analysis where I'd like to discover regions of selective sweeps in a bacterial genome using some sliding window softwares.
I have multiple groupings of bacterial alignments and want to find significant sites of selective sweep events. I want to use SimBac to create alignments that have mutations that occur randomly along the length of a genome that is equivalent for my bacteria's genome length, and compute a selective sweep value for these simulated alignments. This should provide a null distribution to compare against my experimental data.
Since I have multiple alignments, the mutation rate for each one might be different given varying sizes. I was wondering if you knew of a tool that could look at my alignments and generate statistics like mutation rate?