How drive treePL to estimate divergence time under strict global clock model?

[CalamusLiber]

Dear author,

I would like to use treePL to estimate divergence time of a simulated phylogeny under clock model not relaxed one. How can I set the configuration file? I know r8s has LF method with nrates=1, but I have not find the corresponding options in treePL. Or the only way is to set a very large smoothing value, like 100000 or even larger?

Thanks and best wishes, Liang

[blackrim]

This is a feature that would be nice to have. I will go ahead and add it.

[evolucionario]

Agree. It would be nice to use the TreePL machinery to estimate under a strict clock model using full likelihood (no penalty term or smoothing parameter). Those likelihood values would be more easily comparable.

[evolucionario]

So, setting a smoothing value very high would be equivalent to estimate under a strict clock but is there a way of obtaining the log-likelihood value (i.e. without the penalty term)?

[blackrim]

Basically, yes. It will require the rates to be the same

On Wed, Aug 1, 2018 at 5:31 PM Santiago Claramunt [email protected] wrote:

So, setting a smoothing value very high would be equivalent to estimate under a strict clock but is there a way of obtaining the log-likelihood value (i.e. without the penalty term)?

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