Related papers: Tree balance in phylogenetic models
Tree balance plays an important role in phylogenetics and other research areas, which is why several indices to measure tree balance have been introduced over the years. Nevertheless, a formal definition of what a balance index actually is…
Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently…
Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a…
We investigate the use of additional 3D and phylogenetic non-3D tree balance indices for analyzing and monitoring forests using an exemplary "virtual forest" dataset from the Wytham Woods, Oxford, UK. This study assesses 3D model quality,…
Effects like selection in evolution as well as fertility inheritance in the development of populations can lead to a higher degree of asymmetry in evolutionary trees than expected under a null hypothesis. To identify and quantify such…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
Although the analysis of rooted tree shape has wide-ranging applications, notions of tree balance have developed independently in different domains. In computer science, a balanced tree is one that enables efficient updating and retrieval…
Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…
Imbalance in the 3D structure of plants can be an important indicator of insufficient light or nutrient supply, as well as excessive wind, (formerly present) physical barriers, neighbor or storm damage. It can also be a simple means to…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Most real-world classification problems deal with imbalanced datasets, posing a challenge for Artificial Intelligence (AI), i.e., machine learning algorithms, because the minority class, which is of extreme interest, often proves difficult…
We solve a class of optimization problems for (phylogenetic) $X$-trees or their shapes. These problems have recently appeared in different contexts, e.g. in the context of the impact of tree shapes on the size of TBR neighborhoods, but so…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices…
This article presents a new way to understand the descriptive ability of tree shape statistics. Where before tree shape statistics were chosen by their ability to distinguish between macroevolutionary models, the ``resolution'' presented in…