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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
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How to set evolutionary clock #19

Closed maesaar closed 4 years ago

maesaar commented 4 years ago

Is it possible and how to set evolutionary clock for example 3.0x10-5 substitutions per site per year?

xavierdidelot commented 4 years ago

Yes it is possible, for that you need to use the arguments "initMu=..." to set the clock rate and also "updateMu=F" to stop it from being updated. The value you set it to should be express for the whole genome, not per site. So if your genome is of length 1Mbp and you want a clock of 3e-5 per site per year, then you should use "initMu=30"

maesaar commented 4 years ago

Thank you for your answer - works fine and MCMC parameters are also >200, except for mu which is 0. But am I correct that it is due to fact that initMu is set and updateMu is disabled?

xavierdidelot commented 4 years ago

Yes that's right.