• "Cluster" and "Treeview": Created by the team at Stanford University, California, these complimentary programs allow processing and visualization of large data sets using hierarchical clustering, self-organizing maps, k-means clustering, and principal component analysis (http://rana.lbl.gov/EisenSoftware.htm)
• GeneCluster2 GeneCluster 2.0: provides the tools to perform supervised classification, gene selection, and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-near-est neighbours (KNN) algorithms, batch self-organizing maps clustering, and a visualization module.
• The pre-eminent commercial package is GeneSpring 7: Contains normalization tools as well as visualization and analysis programs for performing hierarchical clustering, experiment trees, self-organizing maps, k-means clustering, support vector machines, and principal components analysis (PCA) to aid characterization of the most significant patterns in a given experiment (http:// www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf)
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