EBSP

[elena]

Dear all,

I am using extended bayesian skyline plot analyses for a multilocus data set including two phased nuclear genes and two mitochondrial genes. I have several questions for which I can not find any answer in the tutorial or the BEAST forum. Hope anyone can help me:

- How to combine csv files from multiple runs?
- How to get from that analysis the number of coalescent intervals/groups for my population?
- Is there any further analysis to be done with TRACER (menu Analysis BSP) once you get the output from BEAST?

regards

elena

[Chester Sands]

Dear all,

I'd like to re-ask a question that Paula and Elena asked last year that was not specifically answered.  With ESBP  what is the strategy regarding diploid individuals where both alleles are sequenced?  From looking through the tutorial I am guessing that an allele picked at random from each individual would be one strategy (as gene copies are the important unit, not the individual).  Any other advice?

Cheers

Cheps

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[alexei]

Hi Chester,

I hope that Cambridge is treating you well. You can use both alleles
from each individual sequenced at a nuclear locus. In EBSP there is no
need to have the same number of tips in different gene trees. Just
read each gene in from a separate Nexus alignment. If you wanted to
use less sequences for some reason then random sub-sampling is fine.

Cheers
Alexei

On Aug 10, 1:25 am, Chester Sands <chester.sa...@gmail.com> wrote:
> Dear all,
>
> I'd like to re-ask a question that Paula and Elena asked last year that was not specifically answered.  With ESBP  what is the strategy regarding diploid individuals where both alleles are sequenced?  From looking through the tutorial I am guessing that an allele picked at random from each individual would be one strategy (as gene copies are the important unit, not the individual).  Any other advice?
>
> Cheers
>
> Cheps
>
>
>
>
>
>
>
>
>
> > Dear all,
>
> > I am using extended bayesian skyline plot analyses for a multilocus data set including two phased nuclear genes and two mitochondrial genes. I have several questions for which I can not find any answer in the tutorial or the BEAST forum. Hope anyone can help me:
>
> > - How to combine csv files from multiple runs?
> > - How to get from that analysis the number of coalescent intervals/groups for my population?
> > - Is there any further analysis to be done with TRACER (menu Analysis BSP) once you get the output from BEAST?
>
> > regards
>
> > elena
>
> > --
> > You received this message because you are subscribed to the Google Groups "beast-users" group.

> > To view this discussion on the web visithttps://groups.google.com/d/msg/beast-users/-/S3L1cIfZOjsJ.

> > 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.

[Chester Sands]

HI Alexei, and thanks. No blood on the streets here yet. Hope NZ
remains excitement free.

Could you further clarify if this is the same for *Beast? ie, that for
each locus different individuals and different numbers of gene copies
is acceptable.

Cheers

Cheps

--
"Annual income twenty pounds, annual expenditure nineteen six, result happiness.
Annual income twenty pounds, annual expenditure twenty pounds and six,
result misery." Charles Dickens via Mr Micawber

www.chepsinantarctica.com

[alexei]

Yes, *BEAST can handle different individuals and different number of
gene copies for each loci. If the mode of inheritance is different
(say mito versus nuclear) this has to be explicitly specified in
BEAUti.

(No riots in NZ yet apart from about the price of the Rugby World Cup
replica jerseys being twice as expensive here as overseas -- we take
our rugby very seriously down here)

Alexei

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

[elena]

thanks chester and alexei,

I still no have idea however how to combine csv plots, if there is a way.

thanks for any feedback on this

elena

[alexei]

You can't combine the cvs plots, but you can combine the log files the
generated them (using LogCombiner) and rerun only the
vdanalysis part of the BEAST XML by doing a bit of file editing.

You do this by creating a new BEAST XML file with only the
<VDAnalysis> and <CSVexport> elements inside the <beast> element
(remove everything else). You also need to make sure the <logFileName>
element (inside the VDAnalysis) contains the correct name of the
combined log file. You can then run this shortened BEAST XML file in
BEAST to re-run the VDAnalysis and CSVExport on the combined log file.

Alexei

[Rute Clemente-Carvalho]

Dear Beast users,

I am trying to create a Beauti file with a "tree prior" Coalescent: Bayesian skyline plot.

I don't know how to choose the best prior in "skyline.popSize", and which initial value I have to fill.

My data is composed of shorts fragments of cytochrome b with 370bp, approximately, with around 50 individuals in the population.

I really appreciate if one of you could help me with this...

Thank you in advance, 

R.