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Software - Open Source: ClutrFree Synopsis: ClutrFree is a cluster viewer package available as a Java application. ClutrFree provides essentially the ability to compare microarray clusters issued from different experiments, i.e. the same algorithm used with different parameters or different algorithms. ClutrFree features a procedure to construct a tree from those clusters to infer which ones are more stable among different experiments. Also, ClutrFree displays genes and their memberships along with annotations and ontology. Source code, pre-compiled bytecode, documentation and test datasets are provided. The source code is released under the GNU general public license (GPL). Downloads: Current Version ClutrFree 1.2.4 Java (.jar) version Source code (.tar.gz or .zip) Older Versions clutrfree-1.0 - source code (.tar.gz or .zip) clutrfree-1.0.1 - source code (.tar.gz or .zip) clutrfree-1.1 - java (.jar), or source code (.tar.gz or .zip) clutrfree-1.2 - java (.jar), or source code (.tar.gz or .zip) clutrfree-1.2.1 - java (.jar), or source code (.tar.gz or .zip) ClutrFree 1.2.2 - java (.jar), or source code (.tar.gz or .zip) ClutrFree Demonstration Data Rosetta Compendium Yeast Mutant Gene Expression Data (Generic format): data_demo_generic.tar.gz data_demo_generic.zip Rosetta Compendium Yeast Mutant Gene Expression Data (Bayesian Decomposition format): data_demo_bd.tar.gz data_demo_bd.zip Stanford Yeast Cell Cycle Gene Expression Data (Bayesian Decomposition format): yeast_tree.tar.gz yeast_tree.zip Using ClutrFree with TIGR MeV Sample MEV analysis for the Cho Yeast Cell Cycle Data Set: Zipped compression or Tar archive (Data set reference: Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998; 2:65-73.), and then a link to MeV MeV: MultiExperiment Viewer is available from the following link   Functional Genomics Pipeline (FGDP) to ClutrFree Format Conversion Java (,jar) version Source code (.tar.gz) Documentation: ClutrFree User's Manual clutrfree_user_guide.pdf clutrfree_user_guide.ps.gz Related Software: Bayesian Decomposition - A pattern recognition algorithm which uses Bayesian statistics and Markov chain Monte Carlo sampling to determine the physically significant basis vectors for a data set. Reference: Bidaut G. & Ochs M.F. (2004) ClutrFree: cluster tree visualization and interpretation. Bioinformatics Nov 1;20(16):2869-71. Contact Information: Ghislain Bidaut Biostatistics and Bioinformatics Facilities Fox Chase Cancer Center Philadelphia, PA 19111