Web based tools for comparative genomics analysis:
Tools for network inference (incomplete list - under construction):
networkBMA (Bayesian Model Averaging) - developed by Chris Fraley, Wm. Chad Young, Ka Yee Yeung, Adrian Raftery (with contributions from Kenneth Lo). Relevant manuscript: "Integrating external biological knowledge in the construction of regulatory networks from time-series expression data". Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY.BMC Syst Biol. 2012 Aug 16;6:101.
Tools for clustering and classification:
iBMA - iterativeBMA - developed by Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter