AdjacencyMatrix, SimilarityMatrix, and MatrixComparison are MATLAB programs for analysis of connectome neural networks.  They were written by Adam Bloniarz in 2010.  They allow for simple manipulation of matrices, such as adding them together or multiplying by a constant, analysis of graph properties such as degree distribution, modularity, and so forth, and comparison of connectivity of nodes.  For complete lists of functions, consult the first page of each guide.  