publication . Preprint . 2016

Phylogenetic trees

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert;
Open Access English
  • Published: 17 Nov 2016
Abstract
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 to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.
Subjects
arXiv: Computer Science::Mathematical SoftwareComputer Science::Databases
free text keywords: Quantitative Biology - Populations and Evolution, Mathematics - Algebraic Geometry
Related Organizations
Funded by
NSF| PostDoctoral Research Fellowship
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1401591
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences
,
NSF| Mathematics Research Communities
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1321794
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences
,
NSF| EMSW21-RTG: Developing American Research Leadership in Algebraic Geometry and its Boundaries
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0943832
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences
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