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 duplication display circular display type species images large trees (proteobacteria from NCBI taxonomy) search function protein architecture display expression value display unrooted display type multiple support values
Species colorization and gene duplication display (demo) Circular display type (demo) Species images (demo) Large trees (proteobacteria from NCBI taxonomy) Search function (demo) Protein architecture display (demo) Expression value display Unrooted display type (demo) Multiple support values (demo)


New Features

Archaeopteryx 0.968 beta BG (2012.01.03)

Complete version history

Requirements

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).

Download

Latest version: Archaeopteryx 0.968 beta BG (2012.01.03)

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

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

Sign up for the Archaeopteryx mailing list to be informed of new versions and changes.

Previous versions


Examples

ArchaeopteryxE examples (embedded applet)

ArchaeopteryxA examples (open own frame)

Usage

Answers for some frequently asked questions are (will be) available at aptxevo.

Windows, Apple Macintosh (OS X)

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, Apple Macintosh (OS X)

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 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"

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 -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

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 mailing list to be informed of updates and changes
(probably no more than about one message per month).

Email:

Other Programs for Phylogenetic Tree Display and Analysis

Please let us know if you have a suggestion for this list.

References and Contacts

Han M.V. and Zmasek C.M. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics, 10:356. [PubMed] [BMC Bioinformatics] [PDF]


Financial partner: "24Biz" (Lancaster loans)


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