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MrBayes MCMC quality check (Read 10865 times)
Sep 1st, 2016 at 5:13pm

izwan   Offline
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Hi everyone,

I've been trying to see if it was possible to QC the MCMC convergence generated using the MrBayes plugin in UGENE. I've been using Tracer to view the statistics and MCMC quality when using the BEAUti/BEAST software, and am wondering if the same can be applied to MrBayes (in UGENE). I would like to compare the output of the two software. The user manual doesn't really seem to provide much info on this.

I've come across certain information online that MrBayes generates a statistics file (*.pstat) that contains the stats necessary for this. But, I have never had any first hand experience in using the standalone MrBayes software myself.

Any help would be greatly appreciated.

Reference:
researchgate.net/post/How_to_determine_burnin_generation_and_number_of_chain_in_
MrBayes
« Last Edit: Sep 2nd, 2016 at 3:43pm by Olga Golosova »  
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Reply #1 - Sep 2nd, 2016 at 3:42pm

Olga Golosova   Offline
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Posts: 338
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Hi, izwan!

Unfortunately, the current UGENE version 1.24.2 doesn't keep the statistics files, produced by MrBayes.
However, you may try to find the information you need in the UGENE log right after the MrBayes tool launch.

To view the statistics you should check "TRACE" and "DETAILS" log levels in the UGENE Application Settings. See the screenshots.

 

MrBayes_log.png (103 KB | 353 )
MrBayes_log.png
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