Determination of gene function is particularly problematic when studying large gene families because redundancy limits the ability to experimentally assess the contributions of individual genes. Phylogenomics is a phylogenetic approach used in comparative genomics to predict the biological functions of members of a large gene families by assessing the similarity among gene products. Recently, we reported the development of phylomics databases for 1,508 rice kinases (rice kinase database, RKD) and 769 glycosyltransferases (rice glycosyltransferase database, RGTD) (Cao et al., 2008 Molecular plant; Dardick et al, 2007 Plant Physiology Cao et al, 2011 Bioenergy Research). We have also constructed the following databases: