Table 1 

clusterMaker algorithm implementation notes 

Algorithm 
Description 
Source 
Details 


Hierarchical 
Standard hierarchical clustering as implemented by Eisen[1] 
Cluster 3.0 package from Michiel de Hoon of the University of Tokyo 
Ported by clusterMaker authors from C to Java 


kmeans 
Standard kmeans clustering as implemented by Eisen[1] with the addition of silhouette estimation of k 
Cluster 3.0 package from Michiel de Hoon of the University of Tokyo 
Ported by clusterMaker authors from C to Java. Silhouette implemented by clusterMaker authors. 


kmedoid 
Modification of kmeans from above to use medoid rather than means 
Implemented by clusterMaker authors. Silhouette implemented by clusterMaker authors. 



AutoSOME 
The AutoSOME cluster algorithm [34] 
The distributed AutoSOME implementation 
Ported directly to clusterMaker by AutoSOME author 


Affinity Propagation 
The message passingbased approach to clustering by Frey and Dueck[27] 
Implemented from the algorithm description in the original reference 
Implemented by clusterMaker authors 


Connected Components 
Simple division based on connectivity 
Implemented by clusterMaker authors 



Community (GLay) 
NewmanGirvan[32] community clustering as implemented by Su, et al.[33] 
The original GLay plugin for Cytoscape 
Ported by clusterMaker authors 


MCODE 
Bader and Hogue[4] algorithm for finding modules in PPI networks 
The MCODE Cytoscape plugin 
Ported by clusterMaker authors 


MCL 
Markov clustering algorithm from van Dongen[8,28] that uses random walks to simulate flow 
Implemented from original thesis with reference to C implementation for validation of results. 
Implemented by clusterMaker authors as a parallel algorithm to take advantage of multiple CPU cores. 


SCPS 
Spectral clustering algorithm for BLAST similarity networks[24] 
Implemented from the algorithm description in the original reference using the authors' implementation to validate results 
Implemented by clusterMaker authors 


Transitivity Clustering 
Transitivity based clustering approach from Wittkop, et al.[25] 
Ported from Cytoscape TransClust plugin 
Ported by original TransClust authors 


Morris et al. BMC Bioinformatics 2011 12:436 doi:10.1186/1471210512436 