Related papers: The space of equidistant phylogenetic cactuses
We study extremal properties of finite ultrametric spaces $X$ and related properties of representing trees $T_X$. The notion of weak similarity for such spaces is introduced and related morphisms of labeled rooted trees are found. It is…
We present two algorithms for computing the geodesic distance between phylogenetic trees in tree space, as introduced by Billera, Holmes, and Vogtmann (2001). We show that the possible combinatorial types of shortest paths between two trees…
Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks as they contain both directed as well as undirected edges. While…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
The space $ \ft_n = \C^n/\C $ of $n$ points on the line modulo translation has a natural compactification $ \overline \ft_n $ as a matroid Schubert variety. In this space, pairwise distances between points can be infinite; it is natural to…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
This paper is about geometric and topological properties of a proper CAT(0) space $X$ which is cocompact - i.e. which has a compact generating domain with respect to the full isometry group. It is shown that geodesic segments in $X$ can…
Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We use the language of proper CAT(-1) spaces to study thick, locally compact trees, the real, complex and quaternionic hyperbolic spaces and the hyperbolic plane over the octonions. These are rank 1 Euclidean buildings, respectively rank 1…
This thesis is concerned with equidistant foliations of Euclidean space, i.e. partitions into complete, connected, properly embedded smooth submanifolds. The space of leaves is an Alexandrov space of nonnegative curvature and the canonical…
Scaffolds are the one-dimensional skeleta of high-dimensional flag simplicial complexes of nonpositive curvature. They generalize the phylogenetic trees of Trop G(2,n) to arbitrary $k$, drawing together SL(k)-web bases, affine buildings,…
We give a new proof of a theorem of Loos stating that a Riemannian symmetric space X with rectangular unit lattice is a symmetric R-space. For this we construct explicitly an isometric extrinsically symmetric embedding of X in a Euclidean…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…