Archaeopteryx

Archaeopteryx is a lightweight software application whose purpose is to help you open, alter, and analyze phylogenetic trees.
It can be deployed on all Windows versions out there, provided that you have the Java working environment installed on the target computer.

Portable tool

This is a portable program which comes with with several benefits to your computer. You may run it by simply opening the executable file (there’s no setup included in the process) and copy it on any USB flash drive or other portable devices so you can have it with you all the time.
It does not leave traces in your Windows registry and store other configuration files so you can get rid of it by deleting the package that you have grabbed from the Internet.

Interacting with the GUI

Archaeopteryx reveals a well-structured suite of features. However, this does not necessarily mean that you can decode the dedicated parameters with ease. You need to invest extra time for learning how to make the most out of the application’s capabilities. A help manual is included in the package and includes short descriptions about the program’s features.
Several checkboxes are integrated at the left side of the working environment for helping you display several items on the tree, such as taxonomy code, protein/gene symbol, protein/gene name, confidence value, event, and node name.

Importing/exporting options

The application offers you the possibility to import data from various file formats, such as XML, NHX, NH, NEX, PHY, TRE, TREE, and TOL. In addition, you can add information from a custom URL or web service and read data from TreeBASE, Pfam, and TreeFam. What’s more, you can print or export the information to PDF, PNG, JPG, GIF, or BMP file format.

Analysis tools

Archaeopteryx offers you the possibility to make use of several dedicated utilities in order to colorize branches depending on confidence, delete branch colors, collapse species-specific subtrees, interpret node names as taxonomic scientific names, treat node names as sequence (protein, gene) names, extract taxonomic codes from node names, as well as get detailed taxonomic information.
Other important configuration parameters worth being mentioned enable you to view data as text, Newick, NHX, or Nexus format, adjust the size of the font, perform searches, and show or hide several elements, such as total node sum dependent cladograms, node boxes, scale, and branch length values.
Furthermore, you are allowed to zoom in or out of the generated tree, order the tree by branch length, color a subtree, and launch a web browser to display sequence or taxonomy information.

Final remarks

The bottom line is that Archaeopteryx comes bundled with a comprehensive suite of features for helping you perform analyses of molecular data sets, especially in the field of phylogenomics. It is suitable mostly for professional users.