Related papers: Optimal Phylogenetic Reconstruction from Sampled Q…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
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…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
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…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.'09], building on the…
We give the first {\sl reconstruction algorithm} for decision trees: given queries to a function $f$ that is $\mathrm{opt}$-close to a size-$s$ decision tree, our algorithm provides query access to a decision tree $T$ where: $\circ$ $T$ has…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
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…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems due to the…