Two Novel Closure Rules for Constructing Phylogenetic Super-Networks

Bandelt, H., Dress, A., 1992. A canonical decomposition theory for metrics on a finite set. Adv. Math. 92, 47–05.

Bininda-Emonds, O., 2004. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Computational Biology Series, vol. 4. Kluwer Academy, Dordrecht.

Bryant, D., Moulton, V., 2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21(2), 255–65.

Dress, A., Huson, D.H., 2004. Constructing splits graphs. IEEE/ACM Trans. Comput. Biol. Bioinform. 1, 109–15.

Fitzpatrick, D., Creevey, C., McInerney, J., 2006. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23, 74–5.

Grünewald, S., Forslund, K., Dress, A., Moulton, V., 2007. QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol. Biol. Evol. 24(2), 532–38.

Gusfield, D., Edduh, S., 2004. The fine structure of galls in phylogenetic networks. INFORMS J. Comput. 16(4), 459–69.

Hamed, B.M., 2005. Neighbour-nets portray the Chinese dialect continuum and the linguistic legacy of China’s demic history. Proc. R. Soc. B 272(1567), 1471–954.

Holland, B., Conner, G., Huber, K.T., Moulton, V., 2007. Imputing supertrees and supernetworks from quartets. Syst. Biol. 56(1), 57–7.

Huber, K.T., Moulton, V., 2005. Phylogenetic networks. In: Gascuel, O. (Ed.), Mathematics of Evolution and Phylogeny. Oxford University Press, London

Huber, K.T., Moulton, V., 2006. Phylogenetic networks from multi-labelled trees. J. Math. Biol. 52, 613–32.

Huson, D.H., Bryant, D., 2005. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23(4), 254–67.

Huson, D.H., Dezulian, T., Kloepper, T.K., Steel, M.A., 2004. Phylogenetic super-networks from partial trees. IEEE Trans. Comput. Biol. Bioinform. 1, 151–58.

Huson, D.H., Kloepper, T.H., Lockhart, P.J., Steel, M.A., 2005. Reconstruction of reticulate networks from gene trees, LNBI 3500, pp. 233–49.

Martin, W., Embley, T.M., 2004. Early evolution comes full circle. Nature 431, 134–37.

McBreen, K., Lockhart, P.J., 2006. Reconstructing reticulate evolutionary histories in plants. Trends Plant Sci. 11(8), 389–04.

Meacham, C.A., 1983. The recovery of trees from measures of dissimilarity. In: Hodson, F.R., Kendall, D.G., Tatu, P. (Eds.), Mathematics in the Archaeological and Historical Sciences, pp. 387–95. Edinburgh University Press, Edinburgh.

Morrison, D., 2005. Networks in phylogenetic analysis: new tools for population biology. Int. J. Parasitol. 35, 567–82.

Rivera, M.C., Lake, J.A., 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 43, 152–55.

Semple, C., Steel, M., 2001. Tree Reconstruction Via Closure Operations on Partial Splits, JOBIM 2000, LNCS, vol. 2066, pp. 126–34. Springer, Berlin.

Semple, C., Steel, M., 2003. Phylogenetics. Oxford University Press, London.

Simonson, A.B., Servin, J.A., Skophammer, R.G., Herbold, C.W., Rivera, M.C., Lake, J.A., 2005. Decoding the genomic tree of life. PNAS 102(Suppl. 1), 6608–613.