# 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" (P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu, and R. Yoshida). 2011. doi: 10.1093/sysbio/syr021. LINK. Systematic Biology. Available at http://arxiv.org/abs/0911.0645.
- "A support vector machine based test for incongruence between sets of trees in tree space" (David Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock, R. Yoshida) submitted.
- "Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope" (D. Haws, T. Hodge, and R. Yoshida), to appear in the Bulletin of Mathematical Biology. Available at http://arxiv.org/abs/1004.2073.
- "Experiments with the site frequency spectrum" (Raazesh Sainudiin, Kevin Thornton, Jennifer Harlow, James Booth, Michael Stillman, Ruriko Yoshida, Robert Griffiths, Gil McVean, and Peter Donnelly), 2011, 829-872. Volume 73, issue 4. Bulletin of Mathematical Biology. LINK.
- "Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses" (K. Xu and R. Yoshida), Front. Psychiatry. 2010. doi: 10.3389/fpsyt.2010.00138 Available at http://arxiv.org/abs/1006.4397
- "Statistical Phylogenetic Tree Analysis Using Differences of Means" (with Elissaveta Arnaoudova, David Haws, Peter Huggins, Jerzy W. Jaromczyk, Neil Moore, Chris Schardl and Ruriko Yoshida), Front. Psychiatry volume 1 number 47. doi:10.3389/fnins.2010.0004. Available at http://arxiv.org/abs/1004.2101.
- "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
- The supplement for the paper "Statistical Phylogenetic Tree Analysis Using Differences of Means" can be accessed at PDF

### Software

- GKDEtrees ("Nonparametric Estimation of Gene Tree Distributions"). DOWNLOAD.
- A software GeneOut and data sets for the paper "A support vector machine based test for incongruence between sets of trees in tree space" can be downloaded at http://cophylogeny.net/SVM.php.
- The software for the paper "Statistical Phylogenetic Tree Analysis Using Differences of Means" can be accessed at http://csurs7.csr.uky.edu/phylotree/ and the login is coevolution and passwd is coevolution*
- 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
- Minisymposium MS26 and MS39 on "Algebraic Statistics" at 2010 SIAM Annual Meeting (AN10), July 12-16, 2010, Pittsburgh, Pennsylvania. The David L. Lawrence Convention Center. LINK
- NIMBioS Working Group on Species Delimitation, at National Institute for Mathematical Biological Synthesis at U of Tennessee, Fall 2010 to Summer 2012.
- NIMBioS Working Group on Species Delimitation, at National Institute for Mathematical Biological Synthesis at U of Tennessee, the opening meeting on December 2nd to 4th, 2010.