Here, we provide a number of tools for the integration, analysis and exploration of phenotypes across species. We currently provide these tools: PhenomeNet: PhenomeNet is a cross-species phenotype network in which nodes are compared based on phenotypic similarity. PhenomeBrowser: The PhenomeBrowser is a web-interface to explore the PhenomeNet. PhenomeBLAST: PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. We make both a command-line tool and a web-server available.