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).
Archaeopteryx requires Java version 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.
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:
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".
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: 2015-05-13