The GenMAPP project is no longer funded or actively supported. The last version of GenMAPP was GenMAPP-CS, which is available as a beta version. More information about GenMAPP-CS here.

We recommend the following open-source tools:

PathVisio: PathVisio is a pathway analysis tool that allows you to draw, edit and analyze biological pathways.
GO-Elite: GO-Elite identifies a minimal non-redundant set of biological ontology terms or pathways to describe a particular set of genes or metabolites.
Cytoscape: Cytoscape is a software platform for visualizing complex networks and integrating these with any type of attribute data.
WikiPathways: WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
AltAnalyze: AltAnalyze is an application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting.