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Bibliography on supertree theory and applications

Aho, A. V., Sagiv, Y., Szymanski, T. G., and Ullman, J. D. 1981. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10: 405&emdash;421.

Barthélemy, J.-P., and Janowitz, F. 1991. A formal theory of consensus. SIAM J. Discrete Math. 3: 305&emdash;322.

Barthélemy, J.-P., and McMorris, F. R. 1986. The median procedure for n-trees. J. Classif. 3: 329&emdash;334.

Baum, B. R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41: 3&emdash;10.

Baum, B. R., and Ragan, M. A. 1993. Reply to A.G. Rodrigo’s "A comment on Baum’s method for combining phylogenetic trees". Taxon 42: 637&emdash;640.

Bininda-Emonds, O. R. P., and Bryant, H. N. 1998. Properties of matrix representation with parsimony analyses. Syst. Biol. 47: 497&emdash;508.

Bininda-Emonds, O. R. P., Bryant, H. B., and Russell, A. P. 1998. Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods. Biol. J. Linn. Soc. 64: 101&emdash;133.

Bininda-Emonds, O. R. P., Gittleman, J. L., and Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74: 143&emdash;175.

Bininda-Emonds, O. R. P., S. G. Brady, J. Kim, and M. J. Sanderson. 2001. Scaling of accuracy in extremely large phylogenetic trees. Pacific Symposium on Biocomputing 6:547-558.

Bininda-Emonds, O. R. P.2000. Factors influencing phylogenetic inference: A case study using the mammalian carnivores. Molecular Phylogenetics and Evolution. 16(1):113-126.

Bininda-Emonds, O., and M. J. Sanderson. 2001. An assessment of the accuracy of MRP supertree construction. Syst. Biol. 50:565-579.

Chase, M. W., Soltis, D. E., Olmstead, R. G., Morgan, D., Les, D. H., Mishler, B. D., Duvall, M. R., Price, R. A., Hills, H. G., Qiu, Y. L., Kron, K. A., Rettig, J. H., Conti, E., Palmer, J. D., Manhart, J. R., Sytsma, K. J., Michaels, H. J., Kress, W. J., Karol, K. G., Clark, W. D., Hedren, M., Gaut, B. S., Jansen, R. K., Kim, K. J., Wimpee, C. F., Smith, J. F., Furnier, G. R., Strauss, S. H., Xiang, Q. Y., Plunkett, G. M., Soltis, P. S., Swensen, S. M., Williams, S. E., Gadek, P. A., Quinn, C. J., Eguiarte, L. E., Golenberg, E., Learn, G. H., Graham, S. W., Barrett, S. C. H., Dayanandan, S., and Albert, V. A. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Gard. 80: 528&emdash;580.

Chen, D., O. Eulenstein, D. Fernandez-Baca, and M. Sanderson. 2002. Supertrees by flipping [submitted to RECOMB 2002]

Chen, K., D. Durand, and M. Farach-Colton. 2000. Notung: dating gene duplications using gene family trees. Pp. 96-106 in Proceedings of the Fourth Annual International Conference on Computational Molecular Biology: RECOMB 2000.

Constantinescu, M. 1995. An efficient algorithm for supertrees. J. Classif. 12: 101&emdash;112.

Cotton, J. A., and R. D. M. Page. Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Submitted ms.

Day, W. H. E. 1985. Optimal algorithms for comparing trees with labeled leaves. J. Classif. 2: 7&emdash;28.

De Queiroz, A., M. J. Donoghue, and J. Kim. 1995. "Separate versus combined analysis of phylogenetic evidence." Annu. Rev. Ecol. Syst. 26: 657-681.

Donoghue, M. J. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Mo. Bot. Gard. 81: 405&emdash;418.

Donoghue, M. J., Doyle, J. A., Gauthier, J., Kluge, A. G., and Rowe, T. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20: 431&emdash;460.

Donoghue, M. J., Ree, R. H., and Baum, D. A. 1998. Phylogeny and the evolution of flower symmetry in the Asteridae. Trends Pl. Sci. 3: 311&emdash;317.

Downey, R.G., and M. R. Fellows. 1997. Parameterized Complexity. Springer-Verlag New York

Duret, L., D. Mouchiroud, and M. Gouy. 1994. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Research 22:2360-2365.

Eernisse, D. J., and A. R. Kluge. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10: 1170&emdash;1195.

Estabrook, G. F., and McMorris, F. R. 1980. When is one estimate of evolutionary relationships a refinement of another? J. Math. Biol. 10: 367&emdash;373.

Estabrook, G. F., Johnson, C. S., Jr., and McMorris, F. R. 1975. An idealized concept of the true cladistic character. Math. Biosci. 23: 263&emdash;272.

Estabrook, G. F., Johnson, C. S., Jr., and McMorris, F. R. 1976a. An algebraic analysis of cladistic characters. Discrete Math. 16: 141&emdash;147.

Estabrook, G. F., Johnson, C. S., Jr., and McMorris, F. R. 1976b. A mathematical foundation for the analysis of cladistic character compatibility. Math. Biosci. 29: 181&emdash;187.

Eulenstein, O. 2001 Flipping to Achieve Consensus. DIMACS Tutorial and Workshop on Bioconsensus II. [http://dimacs.rutgers.edu/Workshops/BioconII]

Ewe ns, W. J., and G. R. Grant. 2001. Statistical methods in bioinformatics. Springer, New York.

Farach, M., and Thorup, M. 1994. Optimal evolutionary tree comparison by sparse dynamic programming. In "Proceedings of the 35th annual symposium on foundations of computer science" , pp. 770&emdash;779, IEEE Computer Society Press, Piscataway, NJ.

Farach, M., Przytycka, T., and Thorup, M. 1995. On the agreement of many trees. Inform. Process. Lett. 55: 297&emdash;301.

Finden, C. R., and A. D. Gordon. 1985. Obtaining common pruned trees. J. Classif. 2: 225&emdash;276.

Fleischer, L. 1999. Building chain and cactus representations of all minimum cuts from Hao-Orlin in the same asymptotic run time. Journal of Algorithms 33:51-72.

Garey, M. R., and D. S. Johnson. 1979. Computers and intractability: a guide to the theory of NP-completeness. W. H. Freeman, San Francisco.

Gordon, A. D. 1986. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. J. Classif. 3: 31&emdash;39.

Graham, R. L., and L. R. Foulds. 1982. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Math. Biosci. 60: 133&emdash;142.

Gupta, A, Nishimura, N. 1998. Finding largest subtrees and smallest supertrees. Algorithmica 21:183-210.

Gusfield, D. 1991. Efficient algorithms for inferring evolutionary trees. Networks 21: 19&emdash;28.

Gusfield, D. 1993. Efficient methods for multiple sequence alignment with guaranteed error bounds. Bull. Math. Biol. 55: 141&emdash;154.

Gusfield, D. 1997. Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge University Press, Cambridge.

Harvey, P. H., and Pagel, M. D. 1991. "The comparative method in evolutionary biology," Oxford University Press, Oxford.

Henzinger, M. R., King, V., and T. Warnow. 1999. Constructing a tree from homoemorphic subtrees, with applications to computational evolutionary biology. Algorithmica 24: 1&emdash;13.

Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383: 130&emdash;131.

Huson, D., S. Nettles, and T. Warnow 1999. Disk covering, a fast converging method for phylogenetic tree reconstruction. Comput. Biol. 6:369-386.

Huson, D., S. Nettles, and T. Warnow 1999. Disk covering, a fast converging method for phylogenetic tree reconstruction. Comput. Biol. 6:369-386.

Källersjö, M., Farris, J. S., Chase, M. W., Bremer, B., Fay, M. F., Humphries, C. J., Petersen, G., Seberg, O., and Bremer, K. 1998. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl. Syst. Evol. 213: 259&emdash;287.

Keselman, D., and Amir, A. 1996. Maximum agreement subtree in a set of evolutionary trees&endash;metrics and efficient algorithms. In "Proceedings of the 35th annual symposium on foundations of computer science" , pp. 758&emdash;769, IEEE Computer Society Press, Piscataway, NJ.

Keselman, D., and Amir, A. 1996. Maximum agreement subtree in a set of evolutionary trees&endash;metrics and efficient algorithms. In Proceedings of the 35th annual symposium on foundations of computer science , pp. 758&emdash;769, IEEE Computer Society Press, Piscataway, NJ.

Kim, J. 1998. Large scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47: 43-60.

Kim, J. and B. Salisbury. 2001. A tree obscured by vines: horizontal transfer and the median tree method for estimating species phylogeny. Pacific Symp. Biocomp. 6: 571-582.

Lapointe, F-J., and G. Cucumel. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46:306-312.

Lecointre, G., Philippe, H., Vân Lê, H. L., and Le Guyader, H. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2: 205&emdash;224.

Liu, F.-G. R., M. M. Miyamoto, N. P. Freire, P. Q. Ong, M. R. Tennant, T. S. Young, K. F. Gugel 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789.

Liu, F.-G. R.; Miyamoto, M. M.; Freire, N. P.; Ong, P. Q.; Tennant, M. R.; Young, T. S.; Gugel, K. F. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786-1789.

Maddison, D. R., Swofford, D. L., and Maddison, W. P. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46: 590&emdash;621.

Maddison, D.R. and W. P. Maddison. 1998. The Tree of Life: A multi-authored, distributed Internet project containing information about phylogeny and biodiversity. Internet address: http://phylogeny.arizona.edu/tree/phylogeny.html.

Mad dison, W. P., Donoghue, M. J., and Maddison, D. R. 1984. Outgroup analysis and parsimony. Syst. Zool. 33: 83&emdash;103.

Maidak, B. L., J. R. Cole, C. T. Parker, G. M. Carrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, and C. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171&emdash;173.

Meacham, C. A. 1981. A manual method for character compatibility analysis. Taxon 30: 591&emdash;600.

Miles, D. B., and Dunham, A. E. 1993. Historical perspectives in ecology and evolutionary biology: the use of phylogenetic comparative analyses. Annu. Rev. Ecol. Syst. 24: 587&emdash;619.

Murphy, W. J., E. Eizirek, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O’Brien. 2001. Molecularphylogenetics and the origin of mammals. Nature 409:614-618.

Nakleh, L., U. Roshan, K. St. John, J. Sun, and T. Warnow. 2001. Designing fast converging phylogenetic methods. Bioinformatics 1:1-9

Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford Univ. Press, London.

Novacek, M. J. 2001. Mammalian phylogeny: Genes and supertrees. Current Biology 11:R573-R575.

O. Eulenstein. 2001 Flipping to Achieve Consensus. DIMACS Tutorial and Workshop on Bioconsensus II. [http://dimacs.rutgers.edu/Workshops/BioconII]

Ort olani, A. 1999. Sopts, stripes, tail tips and dark eyes: predicting the function of carnivore colour patterns using the comparative method. Biol. J. Linn. Soc. 67: 433&emdash;476.

Page, R. D. M. 1993. COMPONENT user's manual (version 2.0). Trustees of The Natural History Museum, London.

Page, R. D. M., and E. C. Holmes. 1998. Molecular evolution: a phylogenetic approach. Blackwell, New York.

Page, R. D. M., and J. A. Cotton. 2000. GeneTree: a tool for exploring gene family evolution. Pages 525-536 in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families (D. Sankoff, and J. Nadeau, eds.). Kluwer Academic Publishers, Dordrecht.

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Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1: 53&emdash;58.

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