PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order.

PermutMatrix is a work space designed to graphically explore gene expression data. It relies on the graphical approach introduced by Eisen and also offers several methods for the optimal reorganization of rows and columns of a numerical dataset. For example, several methods are proposed for optimal reorganization of the leaves of a hierarchical clustering tree, along with several seriation or unidimensional scaling methods that do not require any preliminary hierarchical clustering. This program, developed for MS Windows, with MS-Visual C++, has a clear and efficient graphical interface. Large datasets can be thoroughly and quickly analyzed.