Release Notes: The network loading software now accepts a non-portable binary format for fast loading of large networks, easily scaling to 10M arcs per second. MCL can now subcluster a clustering provided on the command line. Programs for querying and altering networks have more options and capabilities, and output formats have been made simpler and more consistent. An OPTICS-style landscape plot can be emitted and colored by cluster membership.
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 clustering program is somewhat faster now, the program for creating networks from tabular data has become more capable, and throughout the suite parallelisation support was improved and streamlined. Graph transformations are now available to many programs in a single specification language, and more transformations have been added.
Release Notes: This release adds a network analysis program that generates statistics at different edge weight cutoffs. The gene expression data parser has been updated, and a mutual k-nearest-neighbour network reduction option was added. Some obscure options were removed and integration between the different clustering and network analysis programs was tightened.
Release Notes: This release improves support for reading and transforming mRNA array data. MCL has acquired an option to sparsify input graphs, and analysis modes have been split off and are now available as a mode in the clm program. A bug introduced in mcl-09-182 in the cluster interpretation routines has been fixed. The mcx program can now compute both node eccentricity and betweenness centrality parallelized over multiple machines and multiple threads. Minor improvements have been made throughout the entire suite of programs.
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: Numerous cleanups in much of the code. Improvements in caching intermediate results.
Release Notes: mcl and a few of its sibling applications now accept a uniform transformation syntax to transform the values from either a label/value stream or an existing graph. Documentation of the various exchange formats was improved and gathered in the mcxio manual page.
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.
Release Notes: mcl now has better dump modes and iterand analysis capabilities to provide an easy interface with visualization programs. The BLAST module no longer requires the macro processor zoem by default, and many sibling analysis applications have received minor improvements.