This page has a collection of papers on the theory of comparing gene and species trees, largely by mathematicians interested in the subject. The papers are available in either Postscript, PDF format, or both. For the latest versions and information on publication, please contact the authors (email and/or Web page address are given below).
K. Chen, D. Durand and M. Farach-Colton. Notung: Dating Gene Duplications using Gene Family Trees RECOMB2000, Fourth Annual International Conference on Computational Molecular Biology, Apr. 2000 (link to original file)
M. T. Hallett and J. Lagergren. (1999) New Algorithms for the Duplication-Loss Problem. Accepted to RECOMB '00, Tokyo, Japan. (ETH Tech. Report given here)
Fellows, M., M. Hallett, and U. Stege (1998) On the Multiple Gene Duplication Problem. Proceedings of the 9th International Symposium on Algorithms and Computation (ISAAC'98), Taejon, Korea, LNCS 1533, pp. 347-356. (link to original file).
M. Fellows, M. Hallett, Ch. Korostensky, and U. Stege. Analogs & Duals of the MAST Problem for Sequences & Trees, Proceedings of the 6th Annual European Sympoium, Venice, Italy, August 1998 (ESA'98)
(link to original file).
Oliver Eulenstein (1996) A Linear Time Algorithm for Tree Mapping
Bin Ma, Ming Li, and Louxin Zhang On Reconstructing Species Trees From Gene Trees In Term Of Duplications And Losses
Eulenstein and Vingron: On the Equivalence of Two Tree Mapping Measures Arbeitspapiere der GMD no. 936, St. Augustin, September 1995.