Diagonalizing the genome I: navigation in tree spaces

Abstract

The orientable cover of the moduli space of real genus zero algebraic curves with marked points is a compact aspherical manifold tiled by associahedra, which resolves the singularities of the space of phylogenetic trees. The resolution maps planar metric trees to their underlying abstract representatives, collapsing and folding an explicit geometric decomposition of the moduli space into cubes. This decomposition endows the resolving space with an interesting canonical pseudometric. The second part of this paper defines a related (stacky) resolution of a space of real quadratic forms, and suggests, perhaps without much justification, that systems of oscillators parametrized by such objects may provide useful models in genomics.