Genetic distance threshold question

[schultzm]

Thanks for the ClusterPicker software. We are using it as part of our Hepatitis A Virus infection cluster detection pipeline (https://github.com/schultzm/HAVIC).

In using it, we are starting to notice the finer details. One of which we are uncertain about. If I set the genetic distance measure as 3/300, so input to the command line as 0.01, will clusterpicker place isolates with for example 0.013 divergence in the same cluster? We have a case where two isolates are 5/367 apart, but in a clade at 100% support. So, these two isolates get clustered into the same cluster, even though this translates to >0.01 divergence. My question then is, if I input the cutoff to cluster picker as a float with four significant digits, say 0.0100, will clusterpicker then recognise that 0.0136239782 (5/367) is in fact greater than 0.0100?

Thanks,