generate an ultrametric starting tree

[DNA_rules]

Hi, I am getting messages from Beast that suggest my starting tree is
not working, i.e., it may not fit the several log-normal calibration
priors I have set. The tree is an ML tree from RAxML and the topology
is very strongly supported. I would like to get this into ultrametric
format and have run into trouble with various options. I see most of
the standard options are available for Mac but I am using Ubuntu
linux. I could not get r8s to compile correctly and am enough of a
novice R user that I'm not sure that APE is doing what I want it to.
Any suggestions on software that will convert my ML tree to
ultrametric appropriate for Beast input that is available for linux
(or even windows)?

Thanks!
Rich Broughton

[Gerald Schneeweiss]

Hi,

this can be done in Mesquite
(http://mesquiteproject.org/mesquite/mesquite.html): trees are
ultranetricised by extending the terminal branches, so interior nodes
fitting a constraint won't be affected.

Best
Gerald

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[Andrew Rambaut]

Hi Rich,

BEAST will automatically make an input tree ultrametric by distorting the branches in a relatively arbitrary way (it will always push nodes backwards in time). The issue is to make sure the resulting node heights fit within any hard bounds of the priors (this is not done automatically). If you are using translated lognormal distributions (or gamma) then the lower tail of the distribution is always non-zero density so you can make a valid starting tree simply by having deep enough node heights. So what I usually do is to replace all branch lengths with a fixed value that is sufficient to ensure all nodes (once made ultrametric) are older than their upper bounds.

Andrew

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___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

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