Release Notes: A major bottleneck was removed from the matrix read routines, implying a substantial speed-up for graphs with more than 100K nodes.
Release Notes: mcl now supports dumping of submatrices for process analysis. The mcxsubs graph extraction application was rewritten and extended. A Solaris compile error was fixed. The mcxdeblast parser accepts a generic line-based label1/label2/score format. The matrix/graph IO library was cleaned up. A simple utility for hierarchical clustering was added.
Release Notes: A facility for retrieving connected components was added in the form of clmclose. GNU-style option parsing was added to mcl, and mcxsubs, for extracting subgraphs and submatrices, was sped up considerably. The code was audited on 64-bit compatibility and saw some general cleansing. Mcl's postprocessing analysis modes were refined.
Release Notes: This release includes a new utility mcxdump for various dump chores. It also provides various documentation updates, and bugfixes for the BLAST parser mcxdeblast, the formatter clmformat, and the matrix assembler mcxassemble. The new --apropos option for mcl outputs a one-line synopsis for all options.
Release Notes: This release improves some of mcl's supporting sibling applications. The parse/assemble/cluster/format pipeline control has been streamlined. Support for parsing the BLAST column format has been added. Some bugs in the output format application have been fixed. Submatrix selection has been extended to support randomized selection of columns and rows.
Release Notes: Overall improvements were made to the mcl framework. The binary format was revived to enable speedier input, which is convenient for very large graphs. clmformat, which provides a cross-linked Web-based view of cluster structure, was sanitized. mcxsubs now supports extraction of block matrices. Some minor fixes and improvements were made to mcl itself.