Phylogenetics in a warm place: computational aspects of the Tropical Grassmannian

Abstract

Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree space, such as the Billera-Holmes-Vogtmann (BHV) space, offer elegant geometric structure but suffer from statistical and computational limitations. An alternative perspective arises from tropical geometry, the tropical Grassmannian tropGr(2,n), introduced by Speyer and Sturmfels, which coincides with phylogenetic tree space. In this paper, we review the structure of the tropical Grassmannian and present algorithmic methods for its computational study, including procedures for sampling from the tropical Grassmannian. Our aim is to make these concepts accessible to evolutionary biologists and computational scientists, and to motivate new research directions at the interface of algebraic geometry and phylogenetic inference.