Archaeopteryx
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). Documentation is here.
Archaeopteryx.js is the official JavaScript-based version of Archaeopteryx for online ("web") visualization and exploration of phylogenetic trees (demo).
New Features
Addition of automated node collapsing based on
node depth
taxonomic rank
Removal of some unneeded options and settings
Documentation & How-To's
Download
Archaeopteryx requires Java version 8 or higher and has been tested on Microsoft Windows (Windows 7 and 10) and various Linux distributions (Mint, openSUSE, Ubuntu). It is not tested on Apple macOS and might be unstable on that platform.
Jar file containing Archaeopteryx 0.9928 beta 2018-07-05 (based on forester 1.050): forester_1050.jar
Example configuration file: _aptx_configuration_file.txt
Other files: examples, configuration files, etc.
Please use the Archaeopteryx Google Group to report problems
Most current version (experimental, might be unstable)
Launching Archaeopteryx
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.
Linux: Alias
To avoid typing, it is easiest to add the following line to the .bashrc (or corresponding) file:
alias aptx='java -Xmx2048m -cp /path/to/forester.jar org.forester.archaeopteryx.Archaeopteryx -c path/to/_aptx_configuration_file'
Typing "aptx" should now start Archaeopteryx.
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)
ToL Response XML Format: the format currently used by the Tree of Life project webservices (input only)
Important note: While Archaeopteryx currently (May 2014) still allows input in NHX format, support for this format is expected to be removed in future versions. Therefore it is strongly recommended to prepare for migration to phyloXML (use phyloxml_converter with -f=dummy option to convert NHX formatted trees to phyloXML).
Mailing List
Please consider joining the Archaeopteryx Google Group to report issues, make suggestions, and be informed of updates and changes.
Source Code
The source code for Archaeopteryx (as application/module of the the open source forester libraries) is available on GitHub.
Other Programs for Phylogenetic Tree Display and Analysis
Hyperbolic display for large trees: HyperTree
Combining and visualizing evidence from different phylogenetic analyses: TreeGraph 2
Online tool for displaying, managing and customizing phylogenetic trees: EvolView
Interactive Tree Of Life: iTOL
Python Environment for Tree Exploration: ETE
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
last updated: 2018-07-05