PhyloNet: a phylogeny toolbox that is mainly aimed at reconstructing and evaluating phylogenetic networks. It currently includes several features such as the RIATA-HGT method for computing HGT events from species/gene tree pairs, the RECOMP method for detecting interspecific recombination in sequence alignments, measures for comparing phylogenetic networks, and many others. To read more and download the tool, please click here.

NEPAL: a tool for phylogenetic network reconstruction and evaluation using the maximum parsimony (MP) and maximum likelihood (ML) criteria. To read more and download the tool, please click here.

PathwayOracle: a tool for analyzing and generating hypotheses about signal transduction networks. To read more and download the tool, please click here.