A quick tutorial on how to install MrBayes on an Ubuntu system.
Step 1. Open Software Centre
Step 2. Search for ‘mrbayes’ and hit enter
Step 3. Click ‘Install’
Or, alternatively, open a terminal and type ‘sudo apt-get install mrbayes’. And to run MrBayes, open up a terminal and type ‘mb’. That’s it. I just spent 15 minutes downloading and compiling the software from source, when it was already done for me. Oh well.
Just a quick note: if you’re running a 64-bit install of MrBayes in parallel, you will probably need to use this page to apply some patches to the source code:
I was having problems getting MrBayes to work on a workstation running 64-bit Ubuntu, but once I started fresh and first applied those patches, things seemed to work without throwing a ‘segmentation fault’ error during the ‘sump’ function.
Turns out setting up and using MrBayes on an Ubuntu system is much easier than I had thought. If all you want is the normal (serial) version of MrBayes, you can just download it from the repositories. However, if you want a serious speed up in the time it takes to get a good result, you can also run it in parallel on a multicore system (that is, pretty much any computer made in the last 4 years). To get it set up and running on Linux, I used some information I found in a forum post. To recap from there:
- Install the parallel libraries you need from the repositories. The package names I used were: mpich2, libmpich2-dev, and libmpich2-1.2, and libreadline6-dev.
- Download the source code file for MrBayes and unarchive it (on Ubuntu you can just right-click and select ‘Extract Here’
- Find the ‘Makefile’ in the source code and change the line that says ‘MPI ?= no’ so that it says ‘MPI = yes’
- Open a terminal, and navigate to the MrBayes folder (e.g. type in ‘cd /path/to/folder/mrbayes-3.1.2/’) and then make the package (type ‘Make’ at the prompt). It might also be a good idea to change the file called ‘mb’ that is created to something like ‘mbpar’ so that you know it’s the parallel version. Also, I needed to make the file executable, so I typed ‘chmod +x mbpar’ to do that.
- Now, you’ll need to create a file in your home folder called ‘.mpd.conf’ with the line MPD_SECRETWORD=<secretword> in it. Change the <secretword> to something else though; it can be pretty much any word you like.
- ‘mpd &’ will launch the MPICH daemon, which needs to be running in order to handle communicating between the different cores.
- After all this, I was able to type ‘mpirun -np 2 /path/to/mrbayes/mbpar’ to run the parallel version of MrBayes in parallel on both cores of my dual core system. If you have more cores, you can always change the -np argument (e.g. to run it using 4 cores, type ‘mpirun -np 4 /path/to/mrbayes/mbpar’)
With the few tests I’ve done so far, I’ve seen about a 80% speed up by just using 2 cores instead of 1. It’s nice not to have to wait nearly so long to get my results. We’ll see what kind of time savings this could bring if I did it on an 8-core computer.