no code implementations • 23 Mar 2024 • Vincent Moulton, Andreas Spillner, Kristina Wicke
This provides a unified framework for many of the various phylogenetic diversity indices used in the literature based on rooted and unrooted phylogenetic trees, generalizations and new proofs for previous results concerning tree-based indices, and a way to define some new phylogenetic diversity indices that naturally arise as affine or projective variants of each other.
no code implementations • 15 Nov 2023 • Katharina T. Huber, Simone Linz, Vincent Moulton, Charles Semple
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e. g., species or individuals in a population).
no code implementations • 22 Aug 2023 • Katharina T. Huber, Leo van Iersel, Vincent Moulton, Guillaume Scholz
In this paper, we consider the complexity of deciding whether or not a given network is proper forest-based, that is, whether it can be formed by adding arcs to some underlying phylogenetic forest which contains the same number of trees as there are roots in the network.
no code implementations • 18 Mar 2022 • Vincent Moulton, Taoyang Wu
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species.
no code implementations • 11 Nov 2021 • Katharina T. Huber, Vincent Moulton, Megan Owen, Andreas Spillner, Katherine St. John
As a corollary, we also obtain an encoding of ranked, rooted $X$-trees in terms of partitions of $X$, which provides an alternative proof that the space of ultrametric trees on $X$ is CAT(0).
no code implementations • 7 Sep 2021 • Andrew Francis, Katharina T. Huber, Vincent Moulton, Taoyang Wu
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another.
no code implementations • 20 Jul 2021 • Katharina T. Huber, Vincent Moulton, Andreas Spillner
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same set~(X) of species.
no code implementations • 21 Jan 2021 • Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami
In this paper, we show that they can be reconstructed from their induced shortest and longest distance matrices.
Combinatorics
