We now include non-coding mutations (calculated via --sample-paths command of matUtils, see here) in the expected versus actual counts. The current amino-acid fitness estimates are unchanged. We still need to add a rule to do the nucleotide fitness estimates, but that should be easy now that we have the counts.
We now include non-coding mutations (calculated via
--sample-pathscommand ofmatUtils, see here) in the expected versus actual counts. The current amino-acid fitness estimates are unchanged. We still need to add a rule to do the nucleotide fitness estimates, but that should be easy now that we have the counts.