6. Setting Up BAMM

6.1. Check your BAMM version

If you have previously downloaded or installed BAMM, you may check which version of BAMM you have using the --version option in bamm:

bamm --version

If bamm is not automatically found by your operating system, you need to specify the directory in which bamm is located:

~/bamm/build/bamm --version

The previous command assumes that bamm is located in the ~/bamm/build directory. If bamm is in your current directory, you may run:

./bamm --version

6.2. Installation from Homebrew (OS X only)

  1. Install Homebrew, if not installed.

  2. Run the following commands:

    brew tap macroevolution/bamm
brew install bamm

    If you’ve installed BAMM before but you want to upgrade to a new version, run:

    brew update
brew upgrade bamm

  3. You may now run bamm from any directory in your system. See Running below and the Quick-start guide to BAMM to learn how to configure and run BAMM.

6.3. Installation from Executable

The compressed file you downloaded contains the executable program only. We recommend that you also download the example files to use as templates for the control files necessary to run BAMM. Go to the Download page to download the examples.

6.3.1. OS X

  1. Download the Mac OS X tar.gz file containing the executable file for BAMM.

  2. This file is a compressed tar.gz file. To uncompress it, open the Terminal application and run the following command from the directory in which BAMM was downloaded (the actual version of BAMM may be different):

    tar -xzf bamm-1.0.0-MacOSX.tar.gz

    This will uncompress the single file bamm into the current directory.

  3. You may copy or move the file bamm to any directory in your system. See Running below and the Quick-start guide to BAMM to learn how to configure and run BAMM.

Note: Test that bamm will run on your system by simply running ./bamm in the directory in which the program is located. If it prints out a message on “Usage”, the BAMM program is working correctly.

6.3.2. Windows

  1. Download the Windows .zip file containing the executable file and required library files for BAMM.
  2. This file is a compressed zip file. Extract the contents of the zip file and move them to a location you can access from the command-line. Note that the DLL files must present together with the bamm.exe file.
  3. Open the command-line program in Windows by clicking on the Start button and typing “cmd” in the search text box. Use the cd command to go to the directory where BAMM is located. See Running below and the Quick-start guide to BAMM to learn how to configure and run BAMM.

Note: Test that bamm will run on your system by simply running bamm in the directory in which the program is located. If it prints out a message on “Usage”, the BAMM program is working correctly.

6.4. Installation from Source

The following instructions assume you are running bash or a similar Unix shell. In Linux and Mac OS X systems, bash is the default shell when you open the Terminal application. We also assume you have Git and CMake installed.

  1. Get the latest version of BAMM:

    git clone https://github.com/macroevolution/bamm.git

    This will create the directory bamm in your current directory.

  2. Go into the bamm directory and create a build directory where the final executable will be created, then go into that directory:

    mkdir build
cd build

  3. Run cmake, and if successful, run make:

    cmake ..
make -j

    The -j option will compile in parallel.

  4. You can run bamm from this directory, or you may wish to install it in a more permanent location:

    sudo make install

    You may now run bamm from any directory in your system. See Running below and the Quick-start guide to BAMM to learn how to configure and run BAMM.

6.5. Running

To run bamm, you should specify a contol file. For example, if your control file is named divcontrol.txt, run the following:

bamm -c divcontrol.txt

Note that if bamm is not installed in a common location, you need to specify the directory in which bamm is located:

~/bamm/build/bamm -c divcontrol.txt

The previous command assumes that bamm is located in the ~/bamm/build directory. If bamm is in your current directory, you may run:

./bamm -c divcontrol.txt

Any file names specified in the control file are relative to the directory in which bamm was called, which may not be the same location where the executable bamm or the control file are located.

Any option in the control file may be overridden in the command-line by prefixing the option name by --, followed by the new value. For example, to set the seed to 1234, run:

bamm -c divcontrol.txt --seed 1234

To set the initial lambda at the root of the tree to 0.05 and the print frequency to 5000, run:

bamm -c divcontrol.txt --lambdaInit0 0.05 --printFreq 5000

When run, BAMM produces a file named run_info.txt that logs the command-line call used, the random seed, the start and end time-stamps, and a list of parameters/options and their values.