1. MANATEE is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.

The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis.

2. TM4: A package of Open Source software programs for Microarray analysis

TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline.

Currently implemented normalization and data analysis algorithms include total-intensity normalization, Lowess (Locfit) normalization, flip-dye consistency checking, replicates analysis, intensity-dependent z-score filtering (slice analysis), etc.

MIDAS is implemented by Java language and thus a platform-independent application. It requires JDK v1.3 or higher. Refer to the included manual for details.

3. TIGR Spotfinder is a software tool designed for Microarray image processing using the TIFF image files generated by most microarray scanners. TIGR Spotfinder was written in C/C++ for PCs running Windows NT/2000/ME/XP.