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. Macintosh computers may have a problem running PhyloGrapher because of the one-button mouse.
The critical characteristics of graphs in general are which dots are connected by which lines.
The basic elements and characteristics of a graph are its: vertex (node), edge, degree of a vertex (the number of edges that touch it), size (number of vertices), path (a route from vertex to vertex), length of the path (number of edges in a path), planar and non-planar graphs (graph is planar if it can be drawn on a plane so that the edges intersect only at the vertices), distance (shortest path), diameter (longest distance between two vertices), isolated vertex (a vertex of degree zero), adjacent vertices (connected by an edge), neighborhood (adjacent vertices) and others (you can check our collection of web links). A tree is a connected graph containing no cycles.
What's New in This Release:
· Minor bug fixing (PhyloGrapher did not work properly if gene ID represented in numeric characters only, e.g. GenBank identifier [GI]).