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..:: Baobab ::..

Last website update: 26/11/08

Current program version 3.31


Baobab is an editor for large phylogenetic trees written in Java.

Tree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier.

Large means that Baobab includes tools to simplify the task of managing heavy dataset (typically dealing with several hundred species).

Java means that Baobab can be run on almost any platform and OS, including Windows, Mac and Unix/Linux.


Here is a list of what Baobab can do:

Baobab's GUI is made of two types of windows (see screenshots section)

  1. The control panel is the main window from which trees can be loaded, saved or even printed. Trees are shown in a table in the bottom and the current selected tree is displayed.
  2. The user can create up to three navigator windows from which almost all edition tasks may be performed. Subtrees displayed in navigators are shown in a distinct color in the control panel.


Copy/Cut/Paste/Delete a subtree.
Subtrees can be load into memory and paste at another place on the same tree, paste onto a different tree or saved as a full tree.
Changing names
Leaf names can be edited or truncated to a particular size. One can easilly remove some particular characters from leaf names too. Inner nodes may have a name too, which can be use to coerce the underlying subtree.
Setting branch lengths and bootstraps.
Attach any data to nodes and leaves
XML files allow the attachment of virtually any kind of data to a tree. Baobab includes an attribute editor that enable the edition of these attributes (see Attributes). Data may be exported for statistical analysis for instance, or even used to color the tree.
Sample a tree
You can randomly create some sample trees of a particular size from a given tree.


Baobab can read Newick, Nexus and XML trees, and write Newick, XML and Pag trees. An interactive XML filter allow you to define the tags used to store the tree, and to select attributes to be loaded with the tree (see Attributes).

Managing data together with trees

Baobab allows you to manage sequence files along with a tree. Supported formats for input and output include Fasta, Mase, Phylip and Clustal. Sequence are stored as attributes, providing their name match the leaf names.

Baobab also can attach data from a spreadsheet in CSV format. Each row name have to match the leaf names, and each column name is considered as an attribute name.

Baobab also include several comparative analysis tools:

Current development

Current development focuses on data management and comparative analysis tools. Here is a list of several TODOs:

Some long-run perspectives:

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