Dear colleagues,
I am having some problems with node dating using substitution rates in MrBayes 3.2.6, even following the example in the program manual.
According to the manual I need to:
1. Set a normal distribution as the prior for the clock rate: e.g. using 0.02 as the mean and 0.005 as the standard deviation assuming the rate is approximately 0.01 ± 0.005 substitutions per site per million years:
MrBayes > prset clockratepr = normal(0.01,0.005)
2. Modify the tree age prior to an exponential distribution with the rate 0.01:
MrBayes > prset treeagepr = exponential(0.01)
When I run the analysis, the program does not recognize the argument “exponential” to modify the age prior:
No valid match for argument “exponential”
Invalid Treeagepr argument
Error when setting parameter “Treeagepr”
I have checked the "Command Reference for MrBayes ver. 3.2.6" and, in fact, “exponential” does not appears as a valid argument for Treeage parameter, so I think it is an error in the manual but I cannot find a way to solve it. .
Does anyone have had such situation before?
Any solution to solve the problem?
Many thanks,
Yoannis
Dear Yoannis
I know MrBayes well and I appreciate it a lot. But I highly recommend you to use BEAST for time estimations based on sequences. Both programs analyse molecular data Bayesian using MCMC. But BEAST is entirely orientated towards rooted, time-measured phylogenies. I have had very good experiences with BEAST using BEAUTi for creating the input file. BEAUTi is a user interface that enable uploading sequence data (nexus formated) and defining all needed parameters (taxa groups, molecular clock (relaxed, strict), substitution model, etc.). Finally, the BEAST software package includes some other programs more such as Tracer (that analyses the log-file of BEAST or MrBayes) and TreeAnnotator (that searches the "best tree" among data obtained from BEAST).
http://beast.bio.ed.ac.uk/
I recommend you to do first a tutorial to learn the application of different programs.
Good luck!
Carolina
Thanks a lot Carolina,
I actually had heard about BEAST but I've never used it. I will try following the tutorial first to understand the program before running my analysis. My only concern is that I have no (trustworthy) data on fossil record for my study group, that's why I'm trying to date the tree using just substitution rates.
Regards!
Yoannis
Dear Yoannis, mutation rate is no problem for BEAST! Use BEAUTi where you have options for clock priors.
Regards
Carolina
Hi Yoannis!
The parameter exponential indeed is not valid for the command prset treeagepr.
The equivalent is prset treeagepr = gamma(1,0.01) to relate your branch lengths not in units of subtitutions per site, but in Ma.
Hope i'm not too late to answer your question
Hi Paz,
Thanks for your answer, it is not too late!
I had not continued with that analysis because I was busy with other things but now I can test your suggestion.
I also want to run the analysis on Beast, we'll see if it makes any difference.
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