Software

Cluster ONE (Clustering with Overlapping Neighborhood Expansion) is a graph clustering algorithm that is able to handle weighted graphs and readily generates overlapping clusters. Owing to these properties, it is especially useful for detecting protein complexes in protein-protein interaction networks with associated confidence values. Cluster ONE is available as a standalone command-line application, or as a plugin to Cytoscape or ProCope.

SCPS is an efficient, user-friendly, scalable and multi-platform implementation of a spectral clustering method for clustering homologous proteins. SCPS also implements connected component analysis and hierarchical clustering, integrates TribeMCL and interfaces with external tools such as Cytoscape and NCBI BLAST. Available for MS Windows, Mac OS X and Linux.

GFam is a command-line tool for automatic annotation of gene families. GFam offers a framework for complete genome initiatives and model organism resources to build domain-based gene families, derive meaningful functional labels and maintain family annotation across genome releases seamlessly. Our approach achieves a unified system for grouping proteins based on evolutionary and functional relationships.

simplyGO is a plugin of the popular Cytoscape platform that allows the user to quickly visualize a biological network and integrate it with GO information by colouring the nodes according to their GO annotation. simplyGO can also calculate Resnik’s semantic similarity measure for a selected sub-graph.