M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

Y. Zhang, Phylophenetic properties of metabolic pathway topologies as revealed by global analysis, BMC Bioinformatics, vol.7, issue.252, pp.1-13, 2006.

S. Schmid, S. Sunyaev, P. Bork, and T. Dandekar, Metabolites: a helping hand for pathway evolution?, Trends in Biochemical Sciences, vol.28, issue.6, pp.336-341, 2003.
DOI : 10.1016/S0968-0004(03)00114-2

C. V. Forst and K. Schulten, Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information, Journal of Computational Biology, vol.6, issue.3-4
DOI : 10.1089/106652799318319

C. V. Forst and K. Schulten, Phylogenetic Analysis of Metabolic Pathways, Journal of Molecular Evolution, vol.52, issue.6, pp.471-489, 2001.
DOI : 10.1007/s002390010178

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.621.9427

M. Heymans and A. K. Singh, Deriving phylogenetic trees from the similarity analysis of metabolic pathways, Bioinformatics, vol.19, issue.Suppl 1, pp.138-146, 2003.
DOI : 10.1093/bioinformatics/btg1018

L. Liao, S. Kim, and J. F. Tomb, Genome Comparisons Based on Profiles of Metabolic Pathway, Sixth International Conference on Knowledge-Based Intelligent Information & Engineering Systems, pp.16-18, 2002.

S. H. Hong, T. Y. Kim, and S. Y. Lee, Phylogenetic analysis based on genome-scale metabolic pathway reaction content, Applied Microbiology and Biotechnology, vol.65, issue.2, pp.203-210, 2004.
DOI : 10.1007/s00253-004-1641-3

D. Aguila, F. X. Aviles, E. Querol, and M. J. Sternberg, Analysis of phenetic trees based on metabolic capabilites across the three domains of life, Journal of Molecular Biology, vol.340

F. Py-lin, E. Coiera, R. Lan, and V. Sintchenko, In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles, BMC Bioinformatics, vol.10, issue.1, pp.86-96, 2009.
DOI : 10.1186/1471-2105-10-86

G. Gupta, A. Liu, and J. Ghost, Automated Hierarchical Density Shaving: A Robust Automated Clustering and Visualization Framework for Large Biological Data Sets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.2, pp.223-237, 2010.
DOI : 10.1109/TCBB.2008.32

F. Psomopoulos and P. Mitkas, Multi Level Clustering of Phylogenetic Profiles, Proceedings of the IEEE International Conference on Bioinformatics and Bioengineering, pp.308-309, 2010.

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575

A. P. Dempster, N. M. Laird, and D. B. Rubin, Maximum Likelihood from Incomplete Data via the EM Algorithm, Journal of the Royal Statistical Society, Series B (Methodological), vol.39

. Stijn-van-dongen, Graph Clustering by Flow Simulation, 2000.