Archaeopteryx is described as '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)'. There are five alternatives to Archaeopteryx for Mac, Windows and Linux. The best alternative is TreeView, which is free. Other great apps like Archaeopteryx are FigTree (Free, Open Source), TreeView X (Free, Open Source), UGENE (Free, Open Source) and Dendroscope (Free).
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program.
TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, .
Researchers studying phylogenetic relationships need software that is able to visualize rooted phylogenetic trees and networks efficiently, increasingly of large datasets involving hundreds of thousands of taxa.