We present two new software tools for biological network analysis. The first tool addresses the problem of visual analysis of network evolution and comparison of networks across species. It provides the capability to visualize consecutive evolutionary stages of protein interaction networks based on phylogenetic information. The second application provides a user-friendly implementation of Affinity Propagation - a general purpose clustering algorithm (Brendan J. Frey and Delbert Dueck, Science 2007). It can be used to identify coherent modules in biological networks. Both applications are implemented as plugins for the widely used Cytoscape network visualization platform.