clusterone_logo 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_logo 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_logo 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.
gossto_logo GOssTo is a Java based semantic similarity calculator. Bundled in the software are the well-known Resnik, Lin, Jian, simUI, simGRASM similarity measures. It features powerful extension capabilities allowing the user to add as many similarity measures as needed. GOssTo is available as a standalone application or through an intuitive web interface.
justclust_logo JustClust is a tool for analysing biological data with cluster analysis. JustClust can handle many formats of data and cluster the data with many state-of-the-art techniques. The aim of JustClust is to provide an easy-to-use application which can perform any analysis on any data.