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K. Liu, S. Raghavan, S. Nelesen, C.R. Linder, and T. Warnow. SATé: a Method for Co-estimation of Multiple Sequence Alignments and Phylogenetic Trees. In preparation.
S. Raghavan, K. Liu, S. Nelesen, C.R. Linder, and T. Warnow. Evaluation of Multiple Sequence Alignment Methods in Large-Scale Phylogeny Inference. Submitted.
K. Liu, S. Nelesen, S. Raghavan, C.R. Linder, and T. Warnow. Barking up the wrong treelength: The impact of gap penalty on alignment and tree accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 7-21, Jan.-Mar. 2009.
PDF S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analyses. Pacific Symposium on Biocomputing 13:15-24, 2008. Auxiliary materials available here.
PDF Warren A. Hunt Jr and Serita M. Nelesen. Phylogenetic Trees in ACL2. Proceedings of the 6th International Workshop on the ACL2 Theorem Prover and its Applications, Seattle, WA, August 15-16, 2006.
PDF Robert S. Boyer, Warren A. Hunt Jr and Serita M. Nelesen. A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. In Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, number 3692 in Lecture Notes in Computer Science, pages 353-364, © Springer Berlin / Heidelberg, 2005.
PDF Robert S. Boyer, Warren A. Hunt Jr and Serita M. Nelesen. A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. The University of Texas at Austin, Department of Computer Sciences. Technical Report TR-05-12. March, 2005.
PDF Eric Smith, Serita Nelesen, David Greve, Matthew Wilding, and Raymond Richards. An ACL2 Library for Bags (Multisets). Proceedings of the 5th International Workshop on the ACL2 Theorem Prover and its Applications, Austin, TX, 2004.