UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments.
EMAP Toolbox is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
The Clique Extracted Ontologies algorithm (CliXO) infers an ontology in the form of a hierarchical, directed acyclic graph (DAG) from pairwise similarity data. Originally developed for inferring gene ontologies from biological gene networks.
NBS is a method for stratification (clustering) of patients within a cancer cohort based on genome scale somatic mutation measurements and a gene interaction network.