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Archaeopteryx (the successor to ATV) is a Java application based on the forester libaries for the visualization of annotated phylogenetic trees. It can be used both as applets (ArchaeopteryxA, ArchaeopteryxE) and as a standalone application. Answers for some frequently asked questions are (will be) available here.
Archaeopteryx requires Sun Java version 5 (also called Java 1.5) or higher.
Archaeopteryx applets (ArchaeopteryxA, ArchaeopteryxE) require the Sun Java plug-in. Most web browsers under Windows and Apple OS X have this already installed. Under Linux, this plug-in might need to be installed, though. For example, under Ubuntu Linux, the Sun 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.
Archaeopteryx has been tested on Windows, Linux, and Apple Macintosh (OS X with Java 1.5.0_13).
Latest version: Archaeopteryx 0.955 beta (2009.11.24)
jar file containing all Archaeopteryx types: » forester.jar
jar file containing only Archaeopteryx applets: » archaeopteryx_applets.jar
example configuration file: » _aptx_configuration_file
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Archaeopteryx mailing list
to be informed of new versions and changes.)
ArchaeopteryxA examples (open own frame)
Answers for some frequently asked questions are (will be) available at aptxevo.
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):
"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"
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 the "-Xms" and "-Xmx" Java command line options.
For example:
"java -Xms32m -Xmx256m -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c path\to\_aptx_configuration_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 -Xms32m -Xmx512m -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.
Archaeopteryx applets manual (ArchaeopteryxA and ArchaeopteryxE)
Certain programs (e.g. MrBayes) 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).
To correctly interpret such internal numbers as support values, check "Internal Numbers Are Confidence Values" under the "Options" menu (in the Archaeopteryx application)
before reading the tree file.
Archaeopteryx (as application/module of the the open source forester libraries) is also available
via SourceForge.
Project name: FORESTER/ATV
http://sourceforge.net/projects/forester-atv/
Please consider joining the Archaeopteryx mailing list to be informed of updates and changes
(probably no more than about one message per month).
Han M.V. and Zmasek C.M. (2009).
phyloXML: XML for evolutionary biology and comparative genomics.
BMC Bioinformatics, 10:356.
[PubMed]
[BMC Bioinformatics]
[PDF]
Zmasek C.M. and Eddy S.R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17, 383-384.
[PubMed]
[Bioinformatics]
[Google Scholar]
Christian M Zmasek | Burnham Institute for Medical Research | cmzmasek yahoo com
Last updated 2009.11.24