General

Botany Array Resource
http://bbc.botany.utoronto.ca
A user friendly web based resource that contains a range of tools for functional genomics and data analysis. It contains t ools for querying data include Expression Browser; generates e-northerns, Expression Angler; fishes for genes with similar expression patterns, Promomer; identifies over represented words in a promoter or group of promoters and at to AGI converter; converts 25k Affy GeneChip IDs into AGI IDs and vice versa.

EBI Services
http://www.ebi.ac.uk/services/services_tree.html
Comprehensive list of all tools and databases available at EBI

EBI Tool Box
http://www.ebi.ac.uk/Tools/
Range of bioinformatics tools for DNA and protein analysis

GABI Tools
http://gabi.rzpd.de/biotools/
A range of tools for sequence analysis and manipulation

TAIR Tools
http://www.arabidopsis.org/tools/
An assortment of Arabidopsis resources including:-
VxInsight- Data mining software that converts gene expression data into 3D mountain terrain maps, making relationships and grouping easy to visualize
Java TreeView - cross-platform gene expression visualization tool for interactive display of clustered microarray data.

VIB Tools
http://www.vib.be/Research/EN/Tools/
Software and databases, including tools for DNA-sequence analysis and primer design, protein-sequence and -structure analysis, micro-array and gene expression analysis, phylogenetics and comparative genomics, sequence alignments and formatting and SPPG (Sequence platform for the Phylogenetic analysis of Plant Genes).