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Current version is 3.31. See the What's new file for details of changes.


Baobab is provided "as is", with the hope it may prove useful. Baobab is distributed under the CeCILL License. See the licence agreement here. CeCILL is a French Free Software license compatible with the GNU General Public License.


Baobab is distributed as an executable jar file. Sources are provided as a zipped directory.


First of all, you need the Java virtual machine to be installed on your system. To run Baobab, you just need the Java Runtime Environment, but version 1.4.0 minimum is required (this version includes tools for XML support). You may download it for free at Sun's website:

To install Baobab, just copy the jar file to a directory where executable files may usually be found on your system (this is c:/Program files/ on Windows© systems, /usr/bin/, /usr/local/bin or /home/user_account/bin on Linux/Unix systems.

Windows recognizes jar-files as true executable, and you generally just have to double-click the file to launch Baobab. If this does not seem to work, or on other systems, launch the command in a terminal emulator:
java -jar Baobab.jar
supposing that Baobab.jar and the java command are accessible from the current path (otherwise use appropriate URLs).

On first launch, Baobab will ask you a few questions about language and OS settings. A .Baobab directory containing configuration files will be created in the user home directory.

Compile from sources

To compile Baobab, you need the Java Development Kit version 1.4.2 minimum.

How to cite Baobab

Baobab v. 1.00 as been published in the Bioinformatics journal:

Dutheil J, Galtier N.
BAOBAB: a Java editor for large phylogenetic trees.
Bioinformatics. 2002 Jun;18(6):892-3.

A PDF version of the article may be found here.

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Author: Julien Dutheil # to @).
Laboratoire Génome, populations, interactions, adaptation,
Université Montpellier II