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Phylogenetic
trees
Hector Baños, Nathaniel Bushek, Ruth Davidson, Elizabeth Gross, Pamela E. Harris, Robert Krone, Colby Long, Allen Stewart and Robert Walker
Vol. 11 (2021), 1–7
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Abstract |
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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. |
Keywords
phylogenetic trees, secant ideals, algebraic statistics,
toric ideals
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Mathematical Subject Classification 2010
Primary: 13P25
Secondary: 05C05, 14M25, 92D15
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Supplementary material |
Milestones
Received: 16 November 2016
Revised: 4 January 2020
Accepted: 8 August 2020
Published: 20 February 2022
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Authors |
| Hector Baños | |
| School of Mathematics Georgia Institute of Technology Atlanta, GA United States |
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| Nathaniel Bushek | |
| Department of Mathematics and
Physics The College of St. Scholastica Duluth, MN United States |
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| Ruth Davidson | |
| Department of Mathematics University of Illinois Urbana-Champaign Urbana, IL United States |
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| Elizabeth Gross | |
| Department of Mathematics University of Hawaii‘i at Manoa Honolulu, HI United States |
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| Pamela E. Harris | |
| Department of Mathematics and
Statistics Williams College Williamstown, MA United States |
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| Robert Krone | |
| Department of Mathematics UC Davis Davis, CA United States |
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| Colby Long | |
| Department of Mathematics and
Computational Sciences The College of Wooster 308 E. University Street Wooster, OH 44691 United States |
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| Allen Stewart | |
| Department of Mathematics Seattle University Seattle, WA United States |
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| Robert Walker | |
| Department of Mathematics University of Wisconsin–Madison Madison, WI United States |
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