New Features

• Addition of automated node collapsing based on
• node depth
• taxonomic rank
• Removal of some unneeded options and settings

Complete version history

Documentation & How-To's

• Archaeopteryx documentation

Download

• Jar file containing Archaeopteryx 0.9920 beta 2016-12-14 (based on forester 1.045): forester_1045.jar
• Example configuration file: _aptx_configuration_file.txt
• Other files: examples, configuration files, etc.
• Please use the Archaeopteryx Google Group to report problems
• Previous versions
• Most current version (experimental, might be unstable; to download right-click on "View Raw" and then "Save link as...")

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)
• 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)
• 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).

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

• Archaeopteryx-js
• Drawgram/Drawtree (PHYLIP)
• 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
• jsPhyloSVG
• Treevolution
• Interactive Tree Of Life: iTOL
• Python Environment for Tree Exploration: ETE
• TreeDyn
• PhyloWidget

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

Reference

Contacts

Christian Zmasek | phyloxml -at- gmail -dot- com