Related papers: First steps toward the geometry of cophylogeny

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…

The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…

Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…

Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…

We consider an evolution algebra which corresponds to a bisexual population with a set of females partitioned into finitely many different types and the males having only one type. We study basic properties of the algebra. This algebra is…

Many recursive functions can be defined elegantly as the unique homomorphisms, between two algebras, two coalgebras, or one each, that are induced by some universal property of a distinguished structure. Besides the well-known applications…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

We study the portraits of isometries of rooted trees - the labelling of the tree, at each vertex, by the permutation of its descendants - in terms of languages. We characterize regularly branched self-similar groups in terms of…

In this work, we explore links between natural homology and persistent homology for the classification of directed spaces. The former is an algebraic invariant of directed spaces, a semantic model of concurrent programs. The latter was…

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…

Since they became observable, neuron morphologies have been informally compared with biological trees but they are studied by distinct communities, neuroscientists, and ecologists. The apparent structural similarity suggests there may be…

Evolution algebras are a special class of non-associative algebras exhibiting connections with different fields of Mathematics. Hilbert evolution algebras generalize the concept through a framework of Hilbert spaces. This allows to deal…

The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

Species' interactions are shaped by their traits. Thus, we expect traits -- in particular, trait (dis)similarity -- to play a central role in determining whether a particular set of species coexists. Traits are, in turn, the outcome of an…

The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…

It is known that there is a Hopf algebra structure on the vector space with basis all heap-ordered trees. We give a new bialgebra structure on the space with basis all permutations and show that there is a direct bialgebra isomorphism…