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.
Each gene or protein on PhyloGrapher's graph is represented as a colored node (vertex) and connected to other nodes (vertices) by lines (edges) of variable thickness and color based on the similarity of genes or proteins (distance matrix). The position of each node in the graph is flexible and adjusted by the user to optimize visualization of the inter-relationships between the nodes. Consequently, the physical distances on the graph between nodes have no information content unlike classical phylogenetic trees. The level of similarity between genes or proteins on PhyloGrapher's graphs is indicated by color and line thickness.
PhyloGrapher is written in Tcl/Tk and works on Unix/Linux or Windows that supports the Tcl/Tk toolkit which can be downloaded for free at tcl.activestate.com. Macintosh computers may have a problem running PhyloGrapher because of the one-button mouse.