Phylogenetic trees
Copyright policy )Phylogenetic trees
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.
- Antioch University Santa Barbara United States
- University of Wisconsin–Oshkosh United States
- Georgia Institute of Technology United States
- Seattle University United States
- University of Illinois Urbana-Champagne United States
Populations and Evolution (q-bio.PE), Commutative rings defined by binomial ideals, toric rings, etc., toric ideals, Trees, Software, source code, etc. for problems pertaining to commutative algebra, phylogenetic trees, Mathematics - Algebraic Geometry, Problems related to evolution, secant ideals, algebraic statistics, FOS: Biological sciences, FOS: Mathematics, Toric varieties, Newton polyhedra, Okounkov bodies, Quantitative Biology - Populations and Evolution, Software, source code, etc. for problems pertaining to combinatorics, Algebraic Geometry (math.AG), Software, source code, etc. for problems pertaining to biology, Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.)
Populations and Evolution (q-bio.PE), Commutative rings defined by binomial ideals, toric rings, etc., toric ideals, Trees, Software, source code, etc. for problems pertaining to commutative algebra, phylogenetic trees, Mathematics - Algebraic Geometry, Problems related to evolution, secant ideals, algebraic statistics, FOS: Biological sciences, FOS: Mathematics, Toric varieties, Newton polyhedra, Okounkov bodies, Quantitative Biology - Populations and Evolution, Software, source code, etc. for problems pertaining to combinatorics, Algebraic Geometry (math.AG), Software, source code, etc. for problems pertaining to biology, Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.)
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