Related papers: Family-joining: A fast distance-based method for c…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
A $B$-tree is a type of search tree where every node (except possibly for the root) contains between $m$ and $2m$ keys for some positive integer $m$, and all leaves have the same distance to the root. We study sequences of $B$-trees that…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
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…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…