Important research efforts are made to characterize mechanisms of biological interest, such as stress tolerance, through gene family studies. The identification of these families allows the functional annotation of genes, as genes belonging to one family are supposed to have similar or related functions. We have developed an online comparative genomics application, GenFam, allowing the user to build custom gene families based on several data sources, to run analysis workflows, and to gather results into a synthetic visualization. It allows displaying functional evidences and evolutive history information through widely used tools and the new algorithm IDEVEN. This algorithm is complementing phylogenetic analyses by using syntenic block data and synonymous mutation rates (dS). The system contains additional modules oriented towards stress response study, such as (differential) gene expression data, functional annotations (gene ontologies), and the identification of specific stress-related cis elements in the promoter regions. The aim of this work is to facilitate knowledge representation and functional inference for scientists working on gene families, and an easier way to link stress-related evidences within a gene family tree. It can therefore highlight adaptive evolution within gene families in relation to stress-prone environments and identify candidate genes for drought tolerance in non-model crops by translational studie.