Related papers: Lassoing and corraling rooted phylogenetic trees

In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…

Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…

Suppose we have a set $X$ consisting of $n$ taxa and we are given information from $k$ loci from which to construct a phylogeny for $X$. Each locus offers information for only a fraction of the taxa. The question is whether this data…

This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…

While robotic manipulation of rigid objects is quite straightforward, coping with deformable objects is an open issue. More specifically, tasks like tying a knot, wiring a connector or even surgical suturing deal with the domain of…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…

In the wood industry, logs are commonly quality screened by discrete X-ray scans on a moving conveyor belt from a few source positions. Typically, the measurements are obtained in a single two-dimensional (2D) plane (a "slice") by a…

Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…

With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

We introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…

Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…

We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…

Conventional graph-based dependency parsers guarantee a tree structure both during training and inference. Instead, we formalize dependency parsing as the problem of independently selecting the head of each word in a sentence. Our model…

In this paper, we study the problem of generating structured objects that conform to a complex schema, with intricate dependencies between the different components (facets) of the object. The facets of the object (attributes, fields,…

We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high…