Phylogenetic trees

Preprint English OPEN
Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert;
(2016)
  • Subject: Quantitative Biology - Populations and Evolution | Mathematics - Algebraic Geometry
    arxiv: Computer Science::Mathematical Software | Computer Science::Databases

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used t... View more
  • References (19)
    19 references, page 1 of 2

    [1] 4ti2 team. 4ti2-a software package for algebraic, geometric and combinatorial problems on linear spaces. Available at www.4ti2.de.

    [2] Elizabeth S. Allman, Sonja Petrovic´, John A. Rhodes, and Seth Sullivant. Identifiability of two-tree mixtures for group-based models. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8:710-722, 2011.

    [3] Elizabeth S. Allman, John A. Rhodes, and Seth Sullivant. When do phylogenetic mixture models mimic other phylogenetic models? Systematic Biology, 61(6):1049-1059, 2012.

    [4] Mara Casanellas and Jesús Fernández-Sánchez. Performance of a new invariants method on homogeneous and nonhomogeneous quartet trees. Molecular Biology and Evolution, 24(1):288-293, 2007.

    [5] S.N. Evans and T.P. Speed. Invariants of some probability models used in phylogenetic inference. Annals of Statistics, 21(1):355-377, 1993.

    [6] J. Felsenstein and J. A. Cavender. Invariants of phylogenies in a simple case with discrete states. Journal of Classification, 4:57-71, 1987.

    [7] D.R. Grayson and M.E. Stillman. Macaulay2, a software system for research in algebraic geoemetry. Available at http://www.math.uiuc.edu/Macaulay2/, 2002.

    [8] J. A. Lake. A rate-independent technique for analysis of nucleaic acid sequences: Evolutionary parsimony. Molecular Biology and Evolution, 4:167-191, 1987.

    [9] Colby Long and Seth Sullivant. Identifiability of 3-class Jukes-Cantor mixtures. Advances in Applied Mathematics, 64:89-110, 3 2015.

    [10] Frederick A. Matsen, Elchanan Mossel, and Mike Steel. Mixed-up trees: the structure of phylogenetic mixtures. Bulletin of Math Biology, 70(4):1115-1139, 2008.

  • Related Organizations (3)
  • Metrics
Share - Bookmark