skygrid

[Tereza]

Hi there,

I'm exploring the multi locus skygrid in the new beast version and so far it seems to be converging okay. However, the tree files are written by locus, there isn't a file combining the results (like in the EBSP) and I'm not sure how to plot the population size function. Any hints on that?

Also, (how) should I inform beauty the ploidy type of my alignments?

Many thanks in advance!

Tereza

[Andrew Rambaut]

The population sizes will be in the main log file. You will need the new version of Tracer to reconstruct this. You can either download the full BEAST source code and compile it or wait a few days and I will post the latest version.

Andrew

On 25 Nov 2013, at 16:37, Tereza <mtct...@gmail.com> wrote:

I'm exploring the multi locus skygrid in the new beast version and so far it seems to be converging okay. However, the tree files are written by locus, there isn't a file combining the results (like in the EBSP) and I'm not sure how to plot the population size function. Any hints on that?

Also, (how) should I inform beauty the ploidy type of my alignments?

---

Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

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

[Tereza]

Hi Andrew,

I need some advice with the stargrid analysis, regarding the root height and cutoff time.
I have fragments that differ considerably in nucleotide substitution rates: 1 mitochondrial (for which I have an available rate), and some nuclear including intron and exons (no rates available). What should I use as cutoff value? In my mind, this value should encompass the root height of the 'slowest' fragment (say, an exon). Does that makes sense?
Beauti 'suggests' a value that I have no idea if its appropriate or where it comes from. But when I do the reconstruction of the skygrid in tracer using this value I get the message that the root height might not be appropriate. When I use a value more like the estimated initial root height, tracer seems to work fine.

I am also not sure of what trace I should use for the root height in the reconstruction. In the same rationale, should I use the trace of the slowest fragment? If I do so, will the analysis still be calibrated according to the provided rate (mitochondrial fragment) or I'll have to rescale it somehow?

Many thanks in advance!

[Mandev Gill]

Hi Tereza,

In general, you want a cutoff value that is a bit greater than the greatest root height.  If you use a cutoff value that is less than the greatest root height, the analysis may not detect certain aspects of the demographic history once you get further back in time than the cutoff value. 

If you have a good idea beforehand of what such a value might be, you can enter it.  Otherwise you can use the value that Beauti suggests.  In either case, once you've completed the analysis, you should compare the cutoff value you used to the estimated root heights.  If the greatest of the estimated root heights is substantially greater than the cutoff value, it would be a good idea to re-run the analysis using the greatest estimated root height as the cutoff value.

For the Skygrid reconstruction, it's advisable to use the trace which gives the greatest estimated root height.  This will ensure that the plot depicts as much of the reconstructed demographic history as possible.

Hopefully that makes sense.  Please let me know if I can help with anything else.  

[Tereza]

I'll try this. Many, many thanks!

2014/1/16 Mandev Gill <mande...@gmail.com>

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