EClerize is an improved force-directed layout algorithm for biological graphs that represent pathways in which the vertices are identified with EC (Enzyme Commission) numbers. The vertices with the same EC class numbers are treated as members of the same cluster. Positions of vertices in clusters are affected by mainly two factors: biological similarity of each vertex in the same cluster and theoretical length between the vertices.

EClerize can be downloaded from Cytoscape's app store.(http://apps.cytoscape.org/apps/eclerize). EClerize uses BioPAX 3 format as input. Sample pathways (Signaling by EGFR, Visual phototransduction and Signaling by ERBB2) and sample sessions (eclerize sample session.cys and EClerize_p53_Akt_Hras.cys) are located in the folder "Sample Data”.

Reference:
H.F. Danacı, R. Cetin Atalay, V. Atalay, “EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes”, Oral Presentation at GLBIO 2017: Great Lakes Bioinformatics Conference, Chicago, USA, May 15-17, 2017.