Least Squares Methods for Equidistant Tree Reconstruction

Preprint English OPEN
Fahey, Conor; Hosten, Serkan; Krieger, Nathan; Timpe, Leslie;
  • Subject: Mathematics - Combinatorics | Mathematics - Commutative Algebra

UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves, also known as the Bergman comp... View more
  • References (21)
    21 references, page 1 of 3

    [1] F. Ardila. Subdominant matroid ultrametrics, Annals of Combinatorics 8 (2004) pp. 379{389.

    [2] F. Ardila and C. Klivans. The Bergman complex of a matroid and phylogenetic trees, Journal of Combinatorial Theory, Ser. B 96 (2006) pp. 38{49.

    [3] W. J. Bruno, N. D. Socci and A. L. Halpern. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction, Molecular Biology and Evolution 17 (1997) pp. 189{197.

    [4] P. Buneman. A note on the metric property of trees, Journal of Combinatorial Theory, Ser. B 17 (1974) pp. 48{50.

    [5] L. L. Cavalli-Sforza, and A. W. F. Edwards. Phylogenetic analysis: Methods and estimation procedures, Evolution 21 (1967) pp. 550{570.

    [6] V. Chepoi and B. Fichet. `1-approximation via subdominants, Journal of Mathematical Psychology 44 (2000) pp. 600{616.

    [7] W. H. E. Day. Computational complexity of inferring phylogenies from distances matrices, Bulletin of Mathematical Biology 49 (1987) pp. 461{ 467.

    [8] J. S. Farris. On the phenetic approach to vertebrate classi cation, in Major Patterns in Vertebrate Evolution, Plenum, New York, 1977.

    [9] J. Felsenstein. Distance methods for inferring phylogenies: A justi cation, Evolution 38 (1984) pp. 16{24.

    [10] J. Felsenstein. Inferring Phylogenies, Sinauer Associates, Inc., Sunderland, Mass., 2004.

  • Metrics
    No metrics available
Share - Bookmark