Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees 


Overview 

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).
 





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


Download


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).


Launching Archaeopteryx

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.


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.


Examples


Archaeopteryx applets (ArchaeopteryxA, ArchaeopteryxE) are supposed to directly run in a web-browserUnfortunately, Firefox is the only major browser which still (consistently) supports/allows Java applets.

ArchaeopteryxA example (opens own window)

ArchaeopteryxE examples (embedded applet)


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: 2016-08-17