Related papers: Distance-based phylogenetic methods around a polyt…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
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…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
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…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a logarithmic sequence-length requirement---improving significantly over previous polynomial bounds for…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Proximity graph-based methods have emerged as a leading paradigm for approximate nearest neighbor (ANN) search in the system community. This paper presents fresh insights into the theoretical foundation of these methods. We describe an…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…