Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees 


Overview 

Archaeopteryx (Google+) 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). It can be used both as a standalone application and a applet (ArchaeopteryxA and ArchaeopteryxE)





New Features

  • Regular expression search
  • Node specific colors and fonts (example)

Complete version history


Documentation


Download


Archaeopteryx requires Java version 1.7 or higher and has been tested on Microsoft Windows (XP and Windows 7) and various Linux distributions (Mint, openSUSE, Ubuntu).
Please sign up for the Archaeopteryx Google Group to be informed of new versions and changes.


Usage

Windows

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.



Examples


Archaeopteryx applets (ArchaeopteryxA, ArchaeopteryxE) require the Oracle Java plug-in. Most web browsers under Windows have this already installed. Under Linux, this plug-in might need to be installed, though. For example, under Mint or Ubuntu Linux, the Java plug-in can be downloaded and installed with the following command: "sudo apt-get install sun-java6-jre sun-java6-plugin".

ArchaeopteryxA example (opens own window)

ArchaeopteryxE examples (embedded applet)


Input and Output Formats


Source Code

The source code for Archaeopteryx (as application/module of the the open source forester libraries) is available on Google code: http://code.google.com/p/forester/


Mailing List

Please consider joining the Archaeopteryx Google Group to be informed of updates and changes
(probably no more than about one message per week).


Other Programs for Phylogenetic Tree Display and Analysis

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


Reference

Han M.V. and Zmasek C.M. (2009)
phyloXML: XML for evolutionary biology and comparative genomics
BMC Bioinformatics, 10:356. [PubMed] [BMC Bioinformatics] [PDF


Contacts

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



last updated: 2014-11-21