Related papers: Species tree estimation using ASTRAL: how many gen…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
Phylogenetic trees represent evolutionary relationships and can be uniquely defined by sets of finite-state biological characteristics. Despite prior work showing that sufficiently large trees can be determined by $r$-state character sets,…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
This paper proposes an adaptive randomization procedure for two-stage randomized controlled trials. The method uses data from a first-wave experiment in order to determine how to stratify in a second wave of the experiment, where the…
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
This paper investigates tree species classification using Sentinel-2 multispectral satellite image time-series. Despite their critical importance for many applications, such maps are often unavailable, outdated, or inaccurate for large…
Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k-9 taxa where k is the TBR (Tree Bisection and Reconnection)…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…