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). 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.


Screenshots






Species colorization and gene duplications Species images Large tree (Proteobacteria from NCBI taxonomy) Protein architecture display Expression value display



New Features

Archaeopteryx 0.9809 A1ST (130314)

  • Improved linking to entries in UniProt and Genbank
  • Launch of BLAST search at NCBI website (given that a suitable sequence identifier is provided in the sequence name or directly as sequence identifier element)
  • Correctly parses Mr. Bayes 3.2.0 output (including confidence standard deviations)
  • Colorization of subtrees via taxonomic rank
  • Inference of ancestral taxonomic information
  • Numerous additional features and minor bug fixes

Complete version history


Documentation

Documentation is available here.



Requirements

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.
Archaeopteryx has been tested on Microsoft Windows (XP and Windows 7) and various Linux distributions (Mint, openSUSE, Ubuntu, etc.).


Download

Latest version: Archaeopteryx 0.988 SR (140415) (based on forester 1.032)

Jar file containing Archaeopteryx:  forester.jar
To download, right-click and then select "Save Link As..." (on Windows), then launch Archaeopteryx by clicking the downloaded "forester.jar" file on your own desktop.

Example configuration file: _aptx_configuration_file.txt

Jar file containing only Archaeopteryx applets (only needed for web developers): archaeopteryx_applets.jar

Please sign up for the Archaeopteryx Google Group to be informed of new versions and changes.

Previous versions



Examples

ArchaeopteryxA example (opens own window)

ArchaeopteryxE examples (embedded applet)



Usage

Answers for some frequently asked questions are (will be) available on this wiki page.

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.


Archaeopteryx applets

A description about how to use Archaeopteryx as Java applet in your own website is available here.


Input and Output Formats


Important Note

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).
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.


Source Code

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/


Mailing List

Please consider joining the Archaeopteryx Google Group to be informed of updates and changes
(probably no more than about one message per week).


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