ARCHAEOPTERYX

Prepared by: Former user (Deleted) and Former user (Deleted)

Tool Name: ATV (A Tree Viewer) is superceded by Archaeopteryx

Homepage: http://www.phylosoft.org/archaeopteryx

Information: http://www.psc.edu/general/software/packages/atv/+ Platforms: Mac OS X, Linux, Windows

Implementation Language: Java / Perl Mailing List: Yes

Purpose: Visualization of annotated phylogenetic trees

Description: Archaeopteryx, the successor to ATV, is a program to visualize and manipulate annotated phylogenetic trees. The user can zoom in and out, collapse sub-trees, or display only a sub-tree. The data associated at a node can be edited. The program can be run as an applet or a stand-alone application. The application is based on the forester libraries.

Inputs/Outputs:

• phyloXML — phylogenetic XML
• 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, Mesquite, 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

Literature: Zmasek, C.M. and S. R. Eddy. 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384. (Source: Phylogeny Programs)

Related Tools: Forester Referenced in the blogosphere: Archaeopteryx is mentioned in this dechronization blog entry.

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