Bayesian Skyline Analysis Issue

[antoine_UCSD]

Hi Beast users,

I'm trying to perform a Bayesian Skyline Analysis (starting with a logfile with the extendedBSP tree model)

I probably made an error in the parameter (see attached screenshot).

Here's the error  message: "Fatal exception (email to authors)Group size 0 should be integer but found: 0.80809...."
Hope there will be a way to fix it!

Thanks for your comments..

Best Regards,

A

[Andrey Yurchenko]

It is not possible to vizualize EBSP with TRACER. You can use TRACER only for BSP or GMRF.  Find a file with .csv  extension in your EBSP output and open it with Exel to  vizualize EBS plot. 

четверг, 7 февраля 2013 г., 6:38:51 UTC+4 пользователь antoine_UCSD написал:

[antoine_UCSD]

Hi Andrey

I wonder if I can find a way to convert BSP value from the csv file to Ne value (because BSP value in my csv output are <1, which does not make sense in term of Ne?)

Thanks for your help.

A

[Andrey Yurchenko]

Hi Antoine! The must overall explanation is that the value on y-axis is a product of Ne*u(mutation rate)*G (generation time).   I have some problems with this issue too because there are only fragmented informations on the questions. Post here please if you  find additional information on this issue.

Best wishes

Andrey

суббота, 23 февраля 2013 г., 5:39:37 UTC+4 пользователь antoine_UCSD написал:

[Andrey Yurchenko]

Also:

http://beast.bio.ed.ac.uk/FAQ#Evolutionary_rates_and_time_scales

суббота, 23 февраля 2013 г., 14:14:23 UTC+4 пользователь Andrey Yurchenko написал:

[antoine chaillon]

Thanks Andrey

Always very interesting to read your post. A tricky question!

I will keep you posted if I found a way to fix it.

Best regards,

A

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[Andrey Yurchenko]

Hello Antoine, I have found something interesting:

from Molecular Ecology Resources (2011) 11, 423–434   Skyline-plot methods for estimating demographic history
from nucleotide sequences

суббота, 23 февраля 2013 г., 19:29:59 UTC+4 пользователь antoine_UCSD написал:

[antoine chaillon]

Looks good! Excellent,

Where does it come from (reference)?

Thanks.

[Andrey Yurchenko]

Molecular Ecology Resources (2011) 11, 423–434 Skyline-plot methods for estimating demographic history
from nucleotide sequences

понедельник, 25 февраля 2013 г., 0:42:16 UTC+4 пользователь antoine_UCSD написал:

[Andrey Yurchenko]

Hello Yan!

You could find full information on this subject in the table 2 in this article in MER: http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.02988.x/full   (Skyline-plot methods for estimating demographic history from nucleotide sequences)

Best regards,

Andrey Yurchenko 

2013/5/1 <huangya...@163.com>

Hi Andrey,

 

I am also quite intersted in the Bayesian Skyline Analysis. But it makes me so depressed on the x and y axis calibration.

I saw your post that you have solved this problem. Could you please show me some information about it?

Thanks a lot!

 

 

All the best,

Yan

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[huangya...@163.com]

[Huang Yan]

Hi Andrey,

 

Thanks a lot for your nice response.

Yes, I read this paper. But I still have no idea about how to calibrate the axes step by step. I have tried to solve this problem for several days.

I am interested in the Type: Mutation rate, with units "mutations/site/year".  Thus  on the skyline plot figure, I'd like to plot my data with the unit of x-axis "years" and y-axis "population size * generattion time".

From referrences, I found the mutation rate is 2% and the generation time is 1 or 2.

So Andrey, now my problem are :

1 do I need using another software to modify the skyline plot with the calibration information? (because I found in TRACE, we could just change the   minimum and maximum Value under  "mannual range" )

2 how can i get the population size * generation time (mine is 1 or 2) on y-axis and years on x-axis? (just with TRACE?)

 

I'll be quite appreciate to you if you would like to give me a hand.

 

Have a nice day,

Yan

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[Andrey Yurchenko]

Dear Yang!
1. You should not use another software for this issue - all
calibration procedure you could do in the Beauty.
2. As I understand, 2% is rate for million year,so in beauty you
should use strict clock and set this clock on 2%/millionyear divided
on 100 (%) and divided on 1000000 to have this callibration in just
years. Finally you set this calibration on 0,00000002. In Tracer you
will have y -axes in years and x -axis in ne *Gen.time.
I think it is right way, but if someone disagree please correct me.

2013/5/2, Huang Yan <huangya...@163.com>:

[Huang Yan]

Hi Andrey,

 

 

Thank you very much for your nice help about calibration problem in skyline plot. And I already get a nice figure.

But there comes another problem.  

I got a population expansion around 100 Kyears ago using skyline model in BEAST. But do you know how to get the exact expansion time? Thanks a lot.

I'll be quite apreciate of you if you would like to help me.

 

Have a nice day,

Yan