Phylogenetic trees are used to demonstrate the evolutionary relationship between species. Previous researches had indicated there is correlation between mutation and physico-chemical properties changes of amino acid. Considering the physico-chemical changes in protein provides additional viewpoints to study process of mutation. A system VirTree has been designed for visualization of ultrametric phylogenetic trees. The system creates a three dimensional view and also provides a virtual reality presentation. The system clusters objects of phylogenetic tree according to physico-chemical property of amino acid while each leaf has its protein sequence. Tree leaves can also be clustered based on structure of tree and branch in which they are located. Adding a new dimension gives advantage to visualize each cluster independently. The algorithm of clustering uses a metric based on wavelet packet transform and classical multidimensional scaling method. In addition to 2-dimensional and 3-dimensional visualizations, the representation of trees in a virtual reality environment is implemented. The virtual reality is provided through Viewlang system. It allows creating interactive 3D graphical applications running in browsers. The virtual reality can dramatically increase the information content of visualization and provides a wide range of view. This allows seeing the overall picture of tree with details while due to limited size of monitor screen this is difficult for large trees by “traditional” methods of visualization.