Research

Here we list some of our publications as well as software we developed and data sets we used.

Publications

• " Bayes estimators for phylogenetic reconstruction" (with P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu). Submitted. Available at http://arxiv.org/abs/0911.0645.
• "Markov Bases of Population Genetic Statistics" (R. Sainudiin, K. Thornton, J. Booth, M. Stillman, and R. Yoshida), submitted.
• "First steps toward the geometry of cophylogeny" (P. Huggins, M. Owen, and R. Yoshida), submitted.
Available at arxiv.org/abs/0809.1908.
• "Geometry of Neighbor-Joining Algorithm for Small Trees" (K. Eickmeyer and R. Yoshida), the proceedings of Algebraic Biology, Springer LNC Series (2008), p82-96. Available at arXiv:0908.0098.
• "A novel test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes" (C. L. Schardl, K. D. Craven, S. Speakman, A. Lindstrom, A. Stromberg, and R. Yoshida). Systematic Biology. Volume 57, Issue 3, (2008), p483 - 498. Available at arXiv:q-bio.PE/0611084.
• "On the optimality of the neighbor-joining algorithm" (K. Eickmeyer, P. Huggins, L. Pachter, and R. Yoshida). Algorithms for Molecular Biology. Volume 3, Issue 5, (2008). (Available at arxiv:0710.5142).
• "Beyond Pairwise Distances: Neighbor Joining with Phylogenetic Diversity Estimates" (D. Levy, R. Yoshida, and L. Pachter), the Molecular Biology and Evolution, 2006 23(3):491-498. MBE site.

Supplement

• Supplement for the paper "First steps toward the geometry of cophylogeny" PDF
• Supplement for the paper "Bayes estimators for phylogenetic reconstruction". See SITE

Software

• The algorithm to sampling pairs of MRCAs only once and data sets. MRCALink.tar.gz
  the algorithm to sampling pairs of MRCAs only once and data sets. The version without LAPACKPP library. samplingData.tar.gz
• This is a software to reconstruct a phylogenetic tree using Bayes estimators for phylogenetic reconstruction ZIP and README file

Data sets

• MRCALink Analysis for Coevolution of Plants and Endophytes. LINK
• Data sets we used for the statistical analysis on gene trees (or host and parasite trees) TARBALL

Meetings and workshops

• Special Session on Advances in Algebraic Statistics at AMS 2010 Spring Southeastern Sectional Meeting Lexington, KY, March 27th-28th, 2010. LINK