ucld.mean prior

[Gideon Pisanty]

I am trying to analyse my data based on the methods given in a previously published paper. They mention the ucld.mean prior, but I can`t find it in any of the BEAUti panels. Does it appear under a different name? Thank you.

[Artem B]

In BEAUti 2 you should set tip dates and then ucld.mean will appears in priors. I don't know why
In BEAUty 1 ucld.mean is in prior without tip dates setting.

[Andrew Rambaut]

The UCLD.mean is the rate of evolution with the relaxed clock. It can be sampled even if there are not tipdates (i.e., all the sequences are from the same time) but it will need to be given an informative prior (perhaps informed from another study).

Andrew

On 14 Dec 2018, at 13:38, Artem B <ui.ar...@gmail.com> wrote:

In BEAUti 2 you should set tip dates and then ucld.mean will appears in priors. I don't know why
In BEAUty 1 ucld.mean is in prior without tip dates setting.

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Andrew Rambaut 

Institute for Evolutionary Biology 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[Artem B]

In BEAUti 2 there is only ucld.stdev if we don't set tip dates

[Andrew Rambaut]

This is correct. Essentially this is saying the rate is fixed to a value of 1. 

In BEAST 1 this is made more explicit by appearing in the prior table but is shown as fixed (it has no operator). If you select a different prior then the operator is turned on and you can sample the rate.

Andrew 

On 15 Dec 2018, at 00:35, Artem B <ui.ar...@gmail.com> wrote:

In BEAUti 2 there is only ucld.stdev if we don't set tip dates

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<Screenshot from 2018-12-15 08-33-15.png>

[Artem B]

Finally I got it! Thanks a lot!
Also thank you for so permanent support, that's great rarity in a case of free programs

[Brandon Stark]

This is not appear unless you using UCLD molecular clock model, if not, you could not find it.

[Gideon Pisanty]

Thank you all for the replies.

Gideon