• SOM: the package GeneSOM written by Jun Yan is available in R. GENECLUSTER 2.0 in Tamayo et al. (56) can be downloaded from

• hierarchical clustering: the R function hclust implements bottom-up hierarchical clustering with several types of linkages.

• k-means: the R function kmeans is based on the algorithm in Hartigan and Wong (82).

• QT_clust proposed in Heyer et al. (83) is implemented by Witold Wolski. It can be accessed from clustering/clustering.html.

• CLARITY proposed in Balasubramaniyan et al. (84) is available upon request from authors.

• The model-based clustering approach in Fraley and Raftery (63) is available as a R package mclust:

• The HMM clustering software GHMM in Schliep et al. (66) and Schliep et al. (67) is available from

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