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Taming-the-BEAST / Skyline-plots

Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.
Creative Commons Attribution 4.0 International
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Byesian Skyline plot #13

Open lentivirus opened 5 months ago

lentivirus commented 5 months ago

Can Bayesian Skyline be performed for 5 HIV-1 pol gene region sequences, for which the tMRCA has been deduced in the backdrop of 200 reference sequences.

laduplessis commented 5 months ago

You can use it, but with only 5 sequences it won't provide anything insightful. For the Bayesian Skyline Plot 5 sequences equate to 4 data points, which is only enough to get a very rough mean Ne estimate, but not enough to estimate changes in Ne over time.