For a given set of pre-aligned nucleic acid or amino acid sequences, MAVL (Multiple Alignment Variation Linker) examines each pair of positions, and determines any pair of identities that occur with greater, or lesser frequency than a simple positional frequency matrix description would predict. The results are returned as a StickWRLD graph, displaying the positional frequency matrix in a graphical form, and providing visual links between positions that have an over, or under-population greater than a user-specified cutoff. The diameter of the visual link is directly related to the percentage of the population that is not explained by the positional frequency matrix.
StickWRLD graph is implemented in Java 3D. Make sure to have Java 3D(TM) API 1.3.1 installed.