1.

P.L. Erdos, M. Steel, L. Székély, and T. Warnow. A few logs suffice to build almost all trees - II. Theoretical Computer Science, 221, pp. 77-118, 1999 (by invitation, special issue of selected papers from ICALP 1997.) (Also appears as DIMACS Technical Report 97-72.) (pdf) (postscript)

2.

D. Huson, S. Nettles, K. Rice, T. Warnow, and S. Yooseph. The Hybrid tree reconstruction method. The Journal of Experimental Algorithmics, Volume 4, Article 5, 1999. Special issue for selected papers from The Workshop on Algorithms Engineering, Saarbrucken, Germany, 1998. (pdf) (postscript)

3.

H.L. Bodlaender, M.R. Fellows, Michael T. Hallett, H. Todd Wareham, and T. Warnow. 2000. The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs, Theoretical Computer Science 244 (2000) 167-188. (This paper contains the results from H. Bodlaender, M. Fellows, and T. Warnow, 1992. Two strikes against perfect phylogeny, Proceedings, International Colloquium on Automata, Languages and Programming. Springer Verlag Lecture Notes in Computer Science, volume 623. pp. 273-283.) (pdf) (postscript)

4.

D. Huson, S. Nettles, and T. Warnow. Disk-Covering, a fast converging method for phylogenetic tree reconstruction. Special issue of the Journal of Computational Biology for selected papers from RECOMB 1999, Vol. 6, No. 3, 1999, pp. 369-386. (This appeared in a preliminary form in the Proceedings of RECOMB 1999, as Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. Lyon, France.) (pdf) (postscript)

Publications appearing in refereed conferences but not journals

1.

J. Kim and T. Warnow. 1999. Tutorial on Phylogenetic Tree Estimation. Intelligent Systems for Molecular Biology, Heidelberg 1999. (pdf) (postscript)

2.

D. Huson, L. Vawter, and T. Warnow. 1999. Solving large scale phylogenetic problems using DCM-2. Proceedings of ISMB (Intelligent Systems for Molecular Biology), (ISMB), Saarbrucken, 1999.

3.

Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman. 2000. "A New Fast Heuristic for Computing the Breakpoint Phylogeny and a Phylogenetic Analysis of a Group of Highly Rearranged Chloroplast Genomes". Proceedings of Intelligent Systems for Molecular Biology (ISMB), August 2000. (pdf) (postscript)

4.

Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman. 2000. An Empirical Comparison Between BPAnalysis and MPBE on the Campanulaceae Chloroplast Dataset. Appears 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, Dordrecht (2000), 99--121. (pdf) (postscript)

5.

Katherine St. John, Tandy Warnow, Bernard M.E. Moret, and Lisa Vawter. 2001. Performance Study of Phylogenetic Methods: (Unweighted) Quartet Methods and Neighbor-Joining. ACM-SIAM Symposium on Discrete Algorithms (SODA) 2001. Invited submission to the Journal of Algorithms, for the special issue of selected papers from SODA 2001. (pdf) (postscript)

6.

Tandy Warnow, Bernard Moret, and Katherine St.~John. 2001. Absolute Convergence: True Trees From Short Sequences. ACM-SIAM Symposium on Discrete Algorithms (SODA) 2001. (pdf) (postscript)

7.

Li-San Wang and Tandy Warnow. 2001. "Estimating true evolutionary distances between genomes," To appear, Symposium on the Theory of Computing (STOC), 2001. (pdf) (postscript)

8.

B. Moret, S. Wyman, D. Bader, T. Warnow, and M. Yan. 2001. Phylogenies from Gene Order Data: A Detailed Study of Breakpoint Analysis. The Pacific Symposium on Biocomputing, 2001, pp. 583-594.

9.

B. Moret, S. Wyman, T. Warnow, and L. Wang. "New approaches for reconstructing phylogenies based on gene order," Intelligent Systems for Molecular Biology, 2001. (pdf) (postscript)

10.

Tandy Warnow, Katherine St. John, Luay Nakhleh, Usman Roshan and Jerry Sun. "Designing Fast Converging Phylogenetic Methods", (presented at ISMB 2001 (Intelligent Systems for Molecular Biology, also appear in special edition of Bioinformatics, Vol. 17 Suppl. 1 2001, pp. S190-S198). (pdf) (postscript)

11.

Tandy Warnow, Katherine St. John, Luay Nakhleh, Usman Roshan and Jerry Sun. "The Performance of Phylogenetic Methods on Trees of Bounded Diameter", 1st Workshop on Algorithms in BioInformatics, 2001. (pdf) (postscript)

12.

L. Wang. "Exact-IEBP: A New Technique For Estimating Evolutionary Distances Between Whole Genomes". To appear, First Workshop on Algorithms in BioInformatics (WABI'01), BRICS, University of Aarhus, Denmark, August 28-31 (2001). (pdf) (postscript)

13.

Tandy Warnow and Ganeshkumar G. . "Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree is Solvable in Polynomial Time", 1st Workshop on Algorithms in BioInformatics, 2001. (pdf) (postscript)

14.

Li-San Wang, Robert Jansen, Bernard Moret, Linda Raubeson, and Tandy Warnow. "Fast Phylogenetic Methods For Genome Rearrangement Evolution: An Empirical Study."Proceedings of Seventh Pacific Symp. of Biocomputing (PSB'02), Hawaii, USA, pp. 524-535, 2002. (postscript)

15.

Luay Nakhleh, Tandy Warnow, Bernard Moret, Katherine St. John, Usman Roshan, and Jerry Sun. "The Accuracy of Fast Phylogenetic Methods for Large Datasets." Proceedings of Seventh Pacific Symp. of Biocomputing (PSB'02), Hawaii, USA, pp. 211-222, 2002. (postscript)

16.

Cara Stockham, Li-San Wang, and Tandy Warnow. "Statistically based postprocessing of phylogenetic analysis by clustering." Accepted by the 10th International Conference of Intelligent Systems and Molecular Biology (ISMB'02), Edmonton Canada, August 2002. (postcript)

17.

Ganeshkumar Ganapathy and Tandy Warnow. "Approximating the complement of the maximum compatible subset of leaves of k trees." To appear, the 5th International Workshop on Approximation Algorithms for Combinatorial Optimization (APPROX'02), September 2002.

18.

Bernard Moret, Usman Roshan, and Tandy Warnow. "Sequence Length Requirements for Phylogenetic Methods." To appear, the Second Workshop on Algorithms in BioInformatics (WABI'02), September 2002. (postcript)

19.

Luay Nakhleh, Usman Roshan, Lisa Vawter, and Tandy Warnow. "Estimating the Devation from a Molecular Clock." To appear, the Second Workshop on Algorithms in BioInformatics (WABI'02), September 2002. (postcript)

20.

"Sequence length requirements for phylogenetic methods", with Bernard Moret, Tandy Warnow, and Usman Roshan in Lecture Notes for Computer Science No 2452 pages 343-356: Proceeding of Second Workshop on Algorithms in BioInformatics (WABI02.), Rome, Italy (2002) (postcript)

21.

Nakhleh, L., Sun, J., Warnow, T., Linder, R., Moret, B.M.E., and Tholse, A., "Towards the development of computational tools for evaluating phylogenetic network reconstruction methods," Proc. 8th Pacific Symp. on Biocomputing (PSB 2003), January 2003. (postscript)