Units of TreeModel.root Height

[rounak vyas]

Hi,
Does anyone know when the calibration of the sequences is done by
specifying the year the sequence was collected, then what are the
units of the treeModel.rootHeight which gives the estimate to the
TMRCA ?
Thanks
Rounak

[Andrew Rambaut]

Years

> --
> You received this message because you are subscribed to the Google Groups "beast-users" group.
> To post to this group, send email to beast...@googlegroups.com.
> To unsubscribe from this group, send email to beast-users...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/beast-users?hl=en.
>
>

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

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[rounak vyas]

Thanks for the reply,
I was not sure about this as BEAST is estimating the root height to be
500 (years) in case of viral data that was taken from a single patient
between 2003 to 2007.
Any suggestions what could be going wrong ?

On Jun 18, 12:11 pm, Andrew Rambaut <a.ramb...@ed.ac.uk> wrote:
> Years
>
> On 18 Jun 2011, at 10:24, rounak vyas wrote:
>
> > Hi,
> > Does anyone know when the calibration of the sequences is done by
> > specifying the year the sequence was collected, then what are the
> > units of the treeModel.rootHeight which gives the estimate to the
> > TMRCA ?
> > Thanks
> > Rounak
>
> > --
> > You received this message because you are subscribed to the Google Groups "beast-users" group.
> > To post to this group, send email to beast...@googlegroups.com.
> > To unsubscribe from this group, send email to beast-users...@googlegroups.com.

> > For more options, visit this group athttp://groups.google.com/group/beast-users?hl=en.

>
> ___________________________________________________________________
>   Andrew Rambaut                
>   Institute of Evolutionary Biology       University of Edinburgh
>   Ashworth Laboratories                         Edinburgh EH9 3JT

>   EMAIL - a.ramb...@ed.ac.uk                TEL - +44 131 6508624      

[Andrew Rambaut]

Dear Rounak,

There are a number of things that could be producing this. Assuming BEAST is converging and mixing OK then look at the substitution rate. What are the HPDs of root height? If they are very large then perhaps there is insufficient information in the data.

You don't say what virus you are looking at but I would guess it is HIV or HCV so you would expect a rate of between 10^-4 to 10^-3, respectively. See if the rate you are getting is much slower. Construct an ML or NJ tree, look at the amount of evolution in these (i.e., average distance from root to tips). This might indicate if some sequences are problematic (out of alignment?) producing very large divergences. You can also load this tree into Pathogen (http://tree.bio.ed.ac.uk/software/pathogen ) to see more formally how well divergence correlates with time of sampling.

Andrew

> For more options, visit this group at http://groups.google.com/group/beast-users?hl=en.
>
>

___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT

EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

[rounak vyas]

Thank you for the reply. 

This is very helpful. I wanted to ask one more thing. I am looking at HIV data and as I mentioned before I have calibrated it for time period between 2003 to 2007. When I do the bayesian skyline construction following the tutorial for BSP posted by you, with slight modification of using a ucld clock instead of strict clock. I get a population prediction from year 1920. How can this be correct ?   

Thank you so much for your help.