Release Notes: The clustering program mcl is now considerably faster due to optimizations in the memory management code. Additionally, it utilises vanilla matrix/vector multiplication where this is faster than sparse matrix/vector multiplication. The speed gains range from slightly below twofold to sixfold depending on graph size and edge density. Large speed increases may be obtained for graphs of sizes up to several hundred thousands of nodes. The graph query program has acquired several edge weight output and summary statistics options, and documentation was fixed and updated.
Release Notes: The mcl suite is moving towards a wider focus on general purpose large scale graph analysis, with the emphasis, besides clustering, on basic graph and clustering measures and transformations. The program mcxarray can now transform tabular gene expression data into graph input. The clm utility computes clustering coefficients, diameter and eccentricity, and betweenness centrality. Many fixes and improvements were made throughout.
Release Notes: MCL can now read label input in a simple line-based format in which each line contains two labels and an optional value, separated by whitespace. Output clusters are returned as lines of tab-separated labels. The BLAST parser can stream this format directly to mcl, creating a concise and easy-to-manage sequence clustering pipeline.