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 • 17 Jul 2023 • Linda Knüver, Mareike Fischer, Marc Hellmuth, Kristina Wicke
For example, for phylogenetic trees, it is common to use balance indices to draw conclusions concerning the underlying evolutionary model, and more than twenty such indices have been proposed and are used for different purposes.
no code implementations • 4 Jul 2022 • Mareike Fischer, Tom Niklas Hamann, Kristina Wicke
However, while non-treelike events need to be taken into account, they are relatively rare, which implies that biologically relevant networks are often assumed to be similar to trees in the sense that they can be obtained by taking a tree and adding some additional edges.
no code implementations • 20 Dec 2021 • Kristina Wicke, Mareike Fischer, Laura Kubatko
In particular, we consider the ranking order of taxa induced by (i) the FP index on a species tree, and (ii) the expected FP index across all gene tree histories associated with the species tree.
no code implementations • 25 Sep 2021 • Mareike Fischer, Lina Herbst, Sophie Kersting, Luise Kühn, Kristina Wicke
We also prove that a few tree shape statistics that have been used to measure tree balance in the literature do not fulfill our definition of an (im)balance index, which might indicate that their properties are not as useful for practical purposes.
no code implementations • 21 Sep 2021 • Sungsik Kong, Joan Carles Pons, Laura Kubatko, Kristina Wicke
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees.
no code implementations • 16 Jul 2021 • Magnus Bordewich, Charles Semple, Kristina Wicke
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa).
no code implementations • 1 Jul 2021 • Mareike Fischer, Andrew Francis, Kristina Wicke
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources.
