Software

R/Bioconductor Packages

• systemPipeR: NGS workflow and report generation environment
• ChemmineR: Cheminformatics Toolkit for R 
• ChemmineOB: R interface to a subset of OpenBabel functionalities 
• fmcsR: Flexible Maximum Common Substructure (FMCS) Searching (also see MCS) 
• eiR: Accelerated similarity searching of small molecules 
• bioassayR: R library for Bioactivity analysis

Command-line

• AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
• BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
• SEED: Clustering next generation sequences
• MCS: A maximum common substructure-based algorithm for searching and predicting drug-like compounds
• EI Search: ultra-fast compound similarity searching

Web Applications

• ChemMine Tools: online tool box for small molecule analysis
• Sub-HMM: identification of conserved protein regions
• EI Search: ultra-fast compound similarity searching

Databases

• ChemMine   (Old Chemical Genetics Page)
• Genome Cluster Database (GCD)  (BLAST)
• Plant Expression Database (PED)
• Plant Unknown-eome Database (POND)
• Cell Wall Navigator (CWN)   (Old Site)
• Cyber Sam