Related papers: Fast Compatibility Testing for Rooted Phylogenetic…
The Rooted Maximum Leaf Outbranching problem consists in finding a spanning directed tree rooted at some prescribed vertex of a digraph with the maximum number of leaves. Its parameterized version asks if there exists such a tree with at…
Dust properties, such as mass and porosity, impact planet formation directly. Understanding the time evolution of dust distribution across multiple properties requires numerical computation. However, available ways to calculate the…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…
In this work, we develop the low-space Massively Parallel Computation (MPC) complexity landscape for a family of fundamental graph problems on trees. We present a general method that solves most locally checkable labeling (LCL) problems…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
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…
Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
We consider the problem of constructing optimal decision trees: given a collection of tests which can disambiguate between a set of $m$ possible diseases, each test having a cost, and the a-priori likelihood of the patient having any…
Multilingual wordlists play a crucial role in comparative linguistics. While many studies have been carried out to test the power of computational methods for language subgrouping or divergence time estimation, few studies have put the data…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…