ExaBayes REST

ExaBayes on XSEDE

ExaBayes is a tool for Bayesian phylogenetic analyses. It implements a Markov chain Monte Carlo sampling approach that allows to determine the posterior probability of a tree (resp., topology) and various evolutionary model parameters, for instance, branch lengths or substitution rates. Similar approaches are implemented in BEAST or MrBayes. ExaBayes has heavily drawn inspiration specifically from the latter one.

ExaBayes comes with the most commonly used evolutionary models, such as the generalized time reversible model (GTR) of character substitution, the discretized \(\Gamma\) model of among site rate heterogeneity and estimates trees with unconstrained branch lengths. For clocked tree models or less parameter-rich substitution models, we refer you to the established tools.

The distinguishing feature of ExaBayes is its capability to handle enormous datasets efficiently. ExaBayes provides an implementation of data parallelism using the Message Passing Interface (MPI). This means, that if you conduct your analysis on a computing cluster composed of several machines (a.k.a. nodes), the memory needed to evaluate the likelihood of trees and parameters given a large alignment can be spread out across multiple computing nodes. In conclusion, the size of the concatenated alignment ExaBayes can handle is only limited by the combined main memory of your entire computing cluster.

Input files: ExaBayes accepts alignment files in a relaxed Phylip format. It can also be configured using a configuration file in Nexus format.

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names Sample File from a Test
input file exabayes_infile.phy
configuration file exabayes_config.nex
   
Sample Output File Type File Name
log file ExaBayes_info.p
tree file(s) ExaBayes_topologies.run-0.p
tree file(s) ExaBayes_topologies.run-0.t
operators file mcmc.operators
   
   

There are several auxiliary programs designed to help with the post-tree analysis of ExaBayes results. These include consense; credibleSet; and postProcParam. Currently we only support consesne, but would add other options on request.

If you use ExaBayes here, please cite:

Aberer, A. J., Kobert, K., and Stamatakis, A. (2014) ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era. Molecular Biology and Evolution 31, 2553-2556

If there is a tool or a feature you need, please let us know

hummingbird in flight

Get 1000 Hours free

On the UCSD Supercomputer

Start Your Trial