General DNA Analysis and Database Tools
EMBL-EBI. Multi-sequence alignment tool.
PLANT GENOME DUPLICATION DATABASE. A good tool for finding synteny or paralogs.
CHROMATIN DATABASE. See an extensive list of genes associated with chromatin related processes.
REPBASE. Multi-species database of repetitive elements. Requires registration.
Publicly Available Arabidopsis Software Tools
TAIR. The basic source of information (not only) for Arabidopsis.
EXPRESSION DATA in eFP BROWSER. Even your grandma will understand gene expression with this tool.
GENEVESTIGATOR. Gene expression analysis center containing more datasets than eFP browser and also several other tools. Requires registration.
GWAPP. Web based GWAs application from the Nordborg lab.
'UCLA Epigenome', 'SALK Epigenome'. Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis at the websites run by the Jacobsen/Pellegrini's labs or the SALK institute, respectively.