Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees


Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.

Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries). Documentation is here.

Archaeopteryx.js is the official JavaScript-based version of Archaeopteryx for online ("web") visualization and exploration of phylogenetic trees (demo).

New Features

  • Addition of automated node collapsing based on

    • node depth

    • taxonomic rank

  • Removal of some unneeded options and settings

Complete version history

Documentation & How-To's


Archaeopteryx requires Java version 8 or higher and has been tested on Microsoft Windows (Windows 7 and 10) and various Linux distributions (Mint, openSUSE, Ubuntu). It is not tested on Apple macOS and might be unstable on that platform.

Launching Archaeopteryx


Clicking on the "forester.jar" file should start it, the configuration file ("_aptx_configuration_file") will be used if it is in the same directory as the jar file.

Unix, Linux, Windows

command line (without use of a configuration file or "_aptx_configuration_file" is in the same directory as the jar file):

"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx"

command line for using a configuration file anywhere in the file system:

"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file"

command line for directly opening a treefile and using a configuration file anywhere in the file system:

"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file treefile"

Increasing memory

Since the Java default memory allocation is quite small, it might by necessary (for trees with more than around 5000 external nodes) to increase the memory which Java can use, with "-Xmx" Java command line option. For example:

"java -Xmx2048m -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_file"

Windows: Batch file

To avoid typing, it is easiest to create at batch (.bat) file. For example create a new file named "aptx.bat" and put a line like this into it:

java -Xmx2048m -cp "C:\path\to\forester.jar" org.forester.archaeopteryx.Archaeopteryx -c "C:\path\to\_aptx_configuration_file"

Clicking on "aptx.bat" should now start Archaeopteryx.

Linux: Alias

To avoid typing, it is easiest to add the following line to the .bashrc (or corresponding) file:

alias aptx='java -Xmx2048m -cp /path/to/forester.jar org.forester.archaeopteryx.Archaeopteryx -c path/to/_aptx_configuration_file'

Typing "aptx" should now start Archaeopteryx.

Input and Output Formats

Mailing List

Please consider joining the Archaeopteryx Google Group to report issues, make suggestions, and be informed of updates and changes.

Source Code

The source code for Archaeopteryx (as application/module of the the open source forester libraries) is available on GitHub.

Other Programs for Phylogenetic Tree Display and Analysis

Please let us know if you have a suggestion for this list.


Han M.V. and Zmasek C.M. (2009)

phyloXML: XML for evolutionary biology and comparative genomics

BMC Bioinformatics, 10:356. [PubMed] [BMC Bioinformatics] [PDF]


Christian Zmasek | phyloxml -at- gmail -dot- com

last updated: 2018-07-05