Databases:
National Center for Biotechnology Information
Phytozome : The JGI Comparative Plant Genomics Portal, a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants.
PlantGDB: Resources for comparative plant genomics.
TAIR: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
OMICtools: A workflow for omic data analysis(NGS, microarray, PCR, MS, NMR)
Bioinformatics:
Bioinformatics Training from the University of California
The R Project for Statistical Computing
Bioconductor: open software for bioinformatics in R
Bowtie 2 : Fast and sensitive read alignment
TopHat : A spliced read mapper for RNA-Seq
Pop's Pipes: Poplar Gene Expression Pipelines
BETA: Binding and Expression Target Analysis
AgriGo: Go analysis Toolkit adn Database for Agriculture Community
Others: