Dendroscope3 is a Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Download installers for Dendroscope3 here: http://www-ab.cs.uni-tuebingen.de/software/dendroscope3 (Alternative download here)
Dendroscope3 requires jloda.
Publication: Daniel H. Huson and Celine Scornavacca, Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks, Syst Biol first published online July 10, 2012 doi:10.1093/sysbio/sys062