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Rob J. de Boer
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In case you refresh during the experiment, i.e. dilute the productively infected cells, provide the dilution factor. One means no dilution, two means a 2-fold dilution (i.e., a continuation of the competition experiment with half of the cells), etcetera.
If you have an estimate of the death rate (delta) of productively infected cells, you should definitely provide this. In case you have no clue, you may enter a zero. This boils down to assuming that there is a selection pressure on the net replication rate of the two variants in the experiment.
We provide two variants of the algorithm. The first assumes that you did a quantative assay providing the percentages of mutant and wild type virus. The second assumes that you sampled a number of sequences, and that you know the number of mutant and wild type sequences. Importantly, since sampling sequences is typically noise, the latter version calculates confidence limits. So either click Percentages or n Samples to continue.
Both versions of the algorithm allow for defining a "restgroup" of irrelevant mutants.