BOL

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements. 

More at http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html