Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields. 1994. Interoperability of biological databases: a meeting report. Syst. Biol. 43:585-589.

Donoghue, M. J. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Missouri Bot. Gard. 81:405-418.

Donoghue, M. J. and D. D. Ackerly. 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. Phil. Trans. R. Soc. London B, 351: 1241-1249.

Maddison, W. P. and D. R. Maddison. 1992. MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0. Sunderland, MA: Sinauer Assoc.

Morell, V. 1996. TreeBASE: the roots of phylogeny. Science 273: 569.

Piel, W. H. 2003. "Phyloinformatics and Tree Networks." In: Wu, C. H., P. Wang, and J. T. L. Wang, eds. Computational Biology and Genome Informatics. World Scientific Press.

Piel, W. H., M. J. Donoghue, and M. J. Sanderson. 2002. "TreeBASE: a database of phylogenetic knowledge." Pp. 41-47. In: Shimura, J., K. L. Wilson, and D. Gordon, eds. To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea. Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.

Piel, W. H., M. J. Sanderson, and M. J. Donoghue. 2003. The Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics. Bioinformatics, 19(9): 1162-1168.

Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson, J. M. Porter, C. Von Dohlen, M. F. Wojciechowski and M. J. Donoghue. 1993. The growth of phylogenetic information and the need for a phylogenetic database. Syst. Biol. 42:562-568.

Sanderson, M. J. and M. J. Donoghue. 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In: Homoplasy and the Evolutionary Process (M. Sanderson and L. Hufford, eds.). San Diego: Academic Press.

Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson. 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. American Journal of Botany, 81(6): 183.

Shan, H., K. G. Herbert, W. H. Piel, D. Shasha and J. T. L. Wang. 2002. A Structure-Based Search Engine for Phylogenetic Databases. Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland, pp. 7-10.

Swofford, D. L. 1993. PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1. Washington, DC: Smithsonian Institution.

Wang, J. T. L., H. Shan, D. Shasha, and W. H. Piel. 2003. TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases. Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003), Cambridge, MA, pp. 171-180.

Wang, J. T. L., H. Shan, D. Shasha and W. H. Piel. 2005. Fast Structural Search in Phylogenetic Databases . Evolutionary Bioinformatics Online, 1: 37-46.