Archaeopteryx Version History

Archaeopteryx version 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

Archaeopteryx version 0.957 beta (2010.09.06):

• Fixed midpoint rooting error.

Archaeopteryx version 0.956 beta (2010.08.16):

• GUI colors controllable via configuration file.

Archaeopteryx version 0.956 beta (2010.06.16):

• Display of orthology and paralogy relationships, thanks to Mathieu Rouard and Guilhem Sempere from Bioversity International
• Inference of ancestral taxonomies (using UniProt Taxonomy database)
• Access to newest version of TreeBASE

Archaeopteryx version 0.955 beta (2009.11.24):

• Minor bug fixes.
• phyloXML validation.

Archaeopteryx version 0.954 beta (2009.10.28):

• (Re)Introduction of tree topology editing (cut, copy, paste, delete, new).
• (Re)Introduction of node data editing.

Archaeopteryx version 0.901 beta (2009.08.21):

• Minor bug-fixes.

Archaeopteryx version 0.900 beta (2009.08.13):

• Addition of overview feature to support navigating large trees (when zoomed in) [example]
• Uses phyloXML version 1.10

version 4.1.04:

• Tabbed display for working with more than one tree at the time, especially in the case of files containing more than one phylogeny [example]
• Enhanced search function: interactive, logical AND and OR, case sensitive/insensitive, partial match/whole terms only [example]
• New tools: taxonomy dependent branch colorization, inference of common parts of scientific names, collapsing of species specific subtrees
• New analysis methods: speciation/duplication inference (SDI algorithm) (application only)
• Web access: access to taxonomic and sequence data (via phyloXML)
• Printing (application only)
• New display options: scale-bar, font selection
• New configuration options: default colors and fonts [example], hiding of menubar and control panel for ArchaeopteryxE applets [example]
• Different display types [examples]

version 4.0.4:

• Webservice support: Direct reading of phylogenies from TreeBASE, TreeFam, and Pfam (application only)

version 4.0.2:

• Webservice support: Direct reading of phylogenies from the Tree of Life project webservices (application only)
• Dynamic hiding of text (depending on zoom level)
• Support for the ToL Response XML Format
• PNG, JPG, and GIF image output (application only)
• ArchaeopteryxE: embedded Archaeopteryx applet [example]
• Interactive subtree colorization
• Reading of zipped phyloXML files (.zip)
• Increased rendering speed: able to handle trees with 5000 external nodes with ease, acceptable at 50 000 external nodes (dynamic hiding on, Java 1.6 with -Xmx256m, 3.8 GHz Pentium 4, Windows XP).
  Test it on the complete 'life on earth' phylogeny from the Tree of Life project: »tol_life_on_earth_1.xml.zip (57124 external nodes), or the »NCBI taxonomy (263691 external nodes) (run Archaeopteryx with increased memory: "java -Xms32m -Xmx512m -cp path\to\forester.jar org.forester.atv.ATV" and use Java 6 Update 10 or higher)

Archaeopteryx | phylosoft | phyloxml