Phylogenetic trees
Hector Ba\~nos, Nathaniel Bushek, Ruth Davidson, Elizabeth Gross,, Pamela E. Harris, Robert Krone, Colby Long, Allen Stewart, and Robert Walker
TL;DR
The paper introduces the PhylogeneticTrees package for Macaulay2, enabling computation of phylogenetic invariants and algebraic properties of group-based tree models in phylogenetics.
Contribution
It provides new computational tools for algebraic analysis of phylogenetic models, including ideal generation and join calculations.
Findings
Computed generating sets for phylogenetic ideals
Calculated lower bounds for ideal dimensions
Demonstrated methods for ideal joins
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.
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