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A free view for gene expressions TreeBuilder3D is a free and open source, interactive viewer that allows organization of SAGE and other types of gene expression data such as microarrays into hierarchical dendrograms, or phenetic networks (the term 'phenetic' used as the analysis relies on principals, used in phylogenetic analysis by system biology).TreeBuilder3D can be used as a visual aid when analyzing differences in expression profiles of SAGE libraries, serves as an alternative to Venn diagrams.Using TreeBuilder3D makes it is possible to load the expression data in the format of plain text files and build a hypothetic tree-like diagram, which describes 'evolutional' relationships between different datasets (such as SAGE libraries). Such diagrams might give one an idea about hierarchical organization of gene expression data, and allow you to associate various expression profiles (represented by SAGE libraries or microarray experiments) with different cellular states or intermediate stages of a decease (such as cancer).The grouping algorithm of TreeBuilder3D is similar to those used in other clustering method, which generally use Pearson and other metrics to group the similar expression profiles. Unlike them, TreeBuilder3D visualizes not only the grouping but also the relative distances between datasets and presents the knowledge about how 'far' or how 'close' expression profiles are to each other. Besides, as it operates with the data in 3D, TreeBuilder3D efficiently removes the constrains of 2D space, giving a possibility to view properly scaled distances between datasets. Requirements: · Java 1.4 or later

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