Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries). Documentation is here.
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).
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.
command line (without use of a configuration file or "_aptx_configuration_file" is
in the same directory as the jar file):
command line for using a configuration file anywhere in the file system:
command line for directly opening a treefile and using a configuration file
anywhere in the file system:
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.
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:
To avoid typing, it is easiest to add the following line to the .bashrc (or corresponding) file:
Please consider joining the Archaeopteryx Google Group to report issues, make suggestions, and be informed of updates and changes.
The source code for Archaeopteryx (as application/module of the the open source forester libraries) is available on GitHub.
Please let us know if you have a suggestion for this list.
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: 2017-02-06