Archaeopteryx (software)
Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics. Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), it also implements the phyloXML format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV). References

External links
phyloXML 
List of phylogeny software, hosted at the University of Washington 
Archaeopteryx

Phylogenetics software