Byesian Skyline plot

[lentivirus]

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]

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.