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 applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application.
Documentation and answers for some frequently asked questions are (will be) available here (some older documentation is also available here), phyloXML related issues might be discussed here.
Documentation is available here.
Archaeopteryx requires Java
version 1.6 or higher. 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". More information is available here.
Latest version: Archaeopteryx 0.988 SR (140415) (based on forester 1.032)
Answers for some frequently asked questions are (will be) available on this wiki page.
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:
A description about how to use Archaeopteryx as Java applet in your own website is available here.
Certain programs produce New Hampshire formatted trees (possibly
inside a Nexus file) where internal tree nodes have both branch length as well as
support values [e.g. "(a:0.1,b:0.2)0.90:0.1"]. By default, Archaeopteryx
interprets these support values (the "0.90" in the example) as node names. In most
situations this is not a big problem, except if the trees are to be rerooted --
then the "support values" move to the wrong branches (because node names are
attached to a node and not to a branch like support values).
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/
Please consider joining the Archaeopteryx Google Group to
be informed of updates and changes
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