The Exelixis Lab


Enabling Research in Evolutionary Biology

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1 Description

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

2 Download & Installation

We distribute binary executables, source code and documentation with examples in one package. ExaBayes supports Linux and MacOS.

We recommend that you build ExaBayes from source code (described in detail in our manual). For convenience, we provide pre-compiled binaries. The multi-threaded binaries work out of the box, if you want to employ parallelism, you require a working MPI installation (also see manual).

For obtaining the correct binaries, please select the appropriate package depending on

  • your operating system,
  • installed MPI version (ignore, if you do not want to run it in parallel),
  • and vector instruction set available on your CPU. If your CPU is not older than 1-2 years, give AVX a try, otherwise SSE should work.

All packages contain the same source files, if you compile yourself, the source-only version is sufficient.

Below is a list of the most recent releases. You can directly track latest changes in the code by checking out our git repository.


Version 1.5 contains a bug fix

version 1.5  
source only tar.gz zip

Version 1.4.1 contains an important bug fix, if you want to run amino acid datasets. Furthermore, branch lengths are linked across all partition by default now.

version 1.4.1 avx sse non-sse
source only tar.gz zip    
Linux, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
Linux, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip
MacOS, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
MacOS, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip

Please consider this announcement about ExaBayes (version 1.4) in the ExaBayes google group.

version 1.4 avx sse non-sse
source only tar.gz zip    
Linux, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
Linux, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip
MacOS, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
MacOS, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip

version 1.3.1 avx sse non-sse
source only tar.gz zip    
Linux, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
Linux, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip

Once more, proper apple support will be postponed until version 1.4. Please let us know, if you urgently need MacOS support.

version 1.3 avx sse non-sse
source only tar.gz zip    
Linux, parallel, open-mpi tar.gz zip tar.gz zip tar.gz zip
Linux, parallel, mpich2 tar.gz zip tar.gz zip tar.gz zip

Binary MacOS packages for version 1.3 will appear soon. Please consider this post in the exabayes mailing list about relevant updates in version 1.3.


version 1.2.1 avx-version sse-version
source only tar.gz zip  
Linux, parallel, open-mpi tar.gz zip tar.gz zip
Linux, parallel, mpich2 tar.gz zip tar.gz zip
MacOS, parallel, open-mpi tar.gz zip tar.gz zip
MacOS, parallel, mpich2 tar.gz zip tar.gz zip
Linux, sequential, no-sse tar.gz zip  
MacOS, sequential, no-sse tar.gz zip  

3 Documentation and Support

A manual is included in the packages available for download. Alternatively, you can directly download the pdf-version or visit the online-version.

You can contact us directly via our google-group (if the link does not work for you, open the link in a new window/tab).

4 Frequently Asked Questions

4.1 Why does execution of ExaBayes fail, while compiling worked fine?

If at runtime you see error messages like this:

./exabayes: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by ./exabayes)
./exabayes: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by ./exabayes)
./exabayes: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./exabayes)

This means, that the wrong version of libc++ gets loaded when you start the program. Possibly you did not use the system's default compiler, but a compiler at a custom location.

Solution: Determine the location of the correct libc++ (e.g., shipped with the compiler) and set LDLIBRARYPATH correctly.

More detailed information is available in our user group.

4.2 Why does compiling with gcc-4.6 fail, although my processor supports AVX?

In this case your compiler fails to generate correct AVX code. Error messages look like this:

/tmp/cc8h9toJ.s:50: Error: no such instruction: `vmovsd (%r15),%xmm1'
/tmp/cc8h9toJ.s:52: Error: no such instruction: `vxorpd %xmm3,%xmm3,%xmm3'

Solution: At the configure stage, use –disable-avx (notice that the code will run slower) or install a more recent version of gcc.

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Author: Andre J. Aberer, Kassian Kobert, Alexandros Stamatakis

Created: 2016-09-23 Fr 00:28

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© The Exelixis Lab 2013 | Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg