Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees (original) (raw)
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 availablehere), phyloXML related issues might be discussed here.
Screenshots
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)
- 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
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.
Examples
ArchaeopteryxE examples (embedded applet)
- Organism images (Images of various fungi and nucleariids are shown, more information is available here)
- Cnidaria (Cnidarian phylogeny from theTree of Life project with 2461 external nodes)
- Mollusk taxonomy (Mollusca from the NCBI taxonomy with 5632 external nodes)
- Multiple support values (Hominidae species tree)
- Wnt (gene tree from TreeFam)
- Apaf-1 (domain architectures)
- Bcl-2 (annotated gene tree)
- Apaf-1 and Bcl-2 (tabbed display)
- Amphibians (Amphibian phylogeny) [same tree displayed differently]
- Various display types
- ArchaeopteryxE without controls and menu
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
- phyloXML – phylogenetic XML (Reference:Han M.V. and Zmasek C.M. (2009): phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10:356)
- New Hampshire/Newick – produced by most major phylogenetic analysis software (e.g. PHYLIP)
- NHX – New Hampshire Extended (deprecated) – our extension of the New Hampshire format
- Nexus – the format used by PAUP*, MrBayes, and many others
- ToL Response XML Format – the format currently used by the Tree of Life project webservices (input only)
- PDF, PNG, GIF, and JPG image output
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: <//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).
Other Programs for Phylogenetic Tree Display and Analysis
- Drawgram/Drawtree (PHYLIP)
- Hyperbolic display for large trees: HyperTree
- Combining and visualizing evidence from different phylogenetic analyses:TreeGraph 2
- jsPhyloSVG
- Treevolution
- Interactive Tree Of Life: iTOL
- Python Environment for Tree Exploration: ETE
- TreeDyn
- PhyloWidget
- PhyloBox
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]
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