We are looking for two postdoctoral fellows to work on computational analysis of the evolution of gene regulation in Drosophila. Click here for more info
Recent Papers
Discordance of gene and species trees in Drosophila
Large-scale turnover of functional transcription-factor binding sites in Drosophila

All software produced by our lab may be downloaded and used free of charge by academic and other non-profit researchers.

Commercial use of the ScanAlyze, Cluster and/or TreeView executable and/or source code requries a license from Stanford University. For information on how to obtain a license, please click here.

Commercial use of the GMEP software requires a license from Lawrence Berkeley National Lab. For information on how to obtain a license, please contact LBNL's Technology Transfer Division.

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Microarray Image Analysis

ScanAlyze [Download] [Previous versions]: Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Written by Michael Eisen. For Windows only. Manual. Source Code.

Current version 2.50. Updated November 27,2002.

Cluster Analysis and Visualization

Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments. Both written by Michael Eisen.

Cluster [Download] [Previous versions]: Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863. For Windows only.

Current version 2.11. .

Manual. Source Code. Demo Data.

Michiel de Hoon of the University of Tokyo has created a version of Cluster (called Cluster 3.0) that implements the same algorithms as my software, but will run on Windows, Mac OS X, Linux and UNIX. It's available here.

FuzzyK [Download]

FuzzyK is a C++ command line program that will perform fuzzy k-means clustering on gene expression data. See Gasch AP and Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3(11), 1-22.

TreeView [Download] [Previous versions]: Graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications. For Windows only.

Current version 1.60. Updated December 6, 2002.

Maple Tree [Download]

Maple Tree is a java-based, open source, cross-platform visualization tool to graphically browse the results of clustering analyses from our Cluster and Fuzzy K clustering software, and many other clustering and analysis programs.

Maple Tree was developed by Lisa Simirenko in our lab.

Combined Expression Data and Sequence Analysis

GMEP [Download] (available for Unix only): Compute genome-mean expression profiles from expression and sequence data. See Chiang et al. Bioinformatics 17(S1):49-55.

Sequence Analysis

GATA [Download] (platform independent): Graphic Alignment Tool for Comparative Sequence Analysis.

GATA was developed by David Nix in our lab.

TFEM [Download](ANSI C code): Transcription Factor Expectation Maximization, an algorithm for detecting DNA regulatory motifs by incorperating positional trends in information content.