GAP is a Java-designed exploratory data analysis (EDA) software for matrix visualization (MV) and clustering of high-dimensional data sets. it provides direct visual perception for exploring structures of a given data matrix and its corresponding proximity matrices, for variables and subjects. Various matrix permutation algorithms and clustering methods with validation indices are implemented for extracting embedded information. GAP has a friendly graphical user interface for easy handling of data and proximity matrices. It is more powerful and effective than conventional graphical methods when dimension reduction techniques fail or when data is of ordinal, binary, and nominal type. (C) 2008 Elsevier B.V. All rights reserved.