Bayesian phylogenetic analysis using MrBayes

MrBayes Plugin

Runs the well known program MrBayes for Bayesian estimation of phylogeny. The output includes your consensus tree along with interactive graphs that display the stats from your run such as likelihood, alpha and kappa.

By Prof. Marc Suchard

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Tree in the toolbar. MrBayes is available as an option at the top of the Tree building options window.


2.2.4 (29 Sep 2017) – Download

– Fixed bug where MrBayes wouldn’t run if there were Chinese characters in the path to the data directory

– Improved NEXUS export performance for very long sequences

– Added an option to skip importing raw trees to improve performance in cases where Geneious runs out of memory after running MrBayes

2.2.3 (10 Mar 2017) – Download

– Fixed a bug where document name would be lost when stripping masked sites

– Fixed rare crash that could occur when cancelling

– Fixed support for macOS 10.6

2.2.2 (11 Apr 2016) – Download

– Fixed crash that would happen when trying to view Posterior output documents created by earlier versions of this plugin

2.2.1 (08 Apr 2016) – Download

– Now compatible with Mac OS X Lion (10.7)

– Now calculates and displays PSRF statistics, using the -sump command. Resulting tables are output in the Raw Posterior Output tab in the Posterior Output document

2.2.0 (10 Feb 2016) – Download

– updated executables to 3.2.6 (MacOSX 32bit not supported any more)

– added support for lg and gtr Rate Matrix

– added lnorm and adgamma to Rate Variations

– changed Branch Lengths: Exponential to GammaDir

– Sequences specified as outgroup have to be referenced by the index instead of the sequence name

– fixed a bug where geneious.nex.mcmc was not created

2.1.3 (14 Oct 2015) – Download

– Fixed loss of some files during long runs

– Improved performance of tree viewer on huge trees

2.1.1 (21 Jun 2015) – Download

– Executables updated to 3.2.2

– Changed option treeagepr = exponential(int) to ~ = gamma(<alpha>, <beta>) to reflect changes in executables

– MrBayes process now stops properly when operation is canceled

2.0.9 (24 Oct 2013) – Download for Geneious 6.1

– Updated bundled binary to 3.2.1

– Added help for enabling CUDA/Beagle with custom binaries

– Fix plugin not importing consensus tree produced by MrBayes

– Properly display non-string attribute values produced by new MrBayes consensus tree

– Better tip attributes for MrBayes consensus tree

– Two MrBayes document types that had same name crashed workflows – make one type

– Cancelling the operation in Geneious did not quit the running MrBayes process on Mac and Linux

2.0.6 (07 Nov 2012) – Download for Geneious 6.0

– Improved memory efficiency

– Forwards compatibility with Geneious 6.0

– Stopped MrBayes crashing when data has duplicate names

2.0.5 (13 Jul 2012) – Download for Geneious 5.5

– Compatibility and stability improvements

2.0.3 (14 Sep 2010) – Download for Geneious 5.1

– Compatibility with Geneious 5.1.1 and later


MrBayes is released under the GNU General Public License and its source code is freely available. More information on citing can be found at


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