Phylogenetic trees
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.
- Publication:
-
arXiv e-prints
- Pub Date:
- November 2016
- DOI:
- 10.48550/arXiv.1611.05805
- arXiv:
- arXiv:1611.05805
- Bibcode:
- 2016arXiv161105805B
- Keywords:
-
- Quantitative Biology - Populations and Evolution;
- Mathematics - Algebraic Geometry
- E-Print:
- J. Softw. Alg. Geom. 11 (2021) 1-7