General Category >> Help and How-to >> MrBayes MCMC quality check

Message started by izwan on Sep 1st, 2016 at 5:13pm

Title: MrBayes MCMC quality check
Post by izwan on Sep 1st, 2016 at 5:13pm
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.


Title: Re: MrBayes MCMC quality check
Post by Olga Golosova on Sep 2nd, 2016 at 3:42pm
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 | 336 )
TRACE_and_DETAILS_checked.png (68 KB | 336 )

UGENE Forum » Powered by YaBB 2.5 AE!
YaBB Forum Software © 2000-2010. All Rights Reserved.