Related papers: Identifiability of 2-tree mixtures for group-based…

Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…

We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree…

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…

Species interaction networks are a powerful tool for describing ecological communities; they typically contain nodes representing species, and edges representing interactions between those species. For the purposes of drawing abstract…

More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer.…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model. In particular, every cycle of size at least 4 and every…

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…

Identifiability concerns finding which unknown parameters of a model can be estimated from given input-output data. If some subset of the parameters of a model cannot be determined given input-output data, then we say the model is…

The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between…

Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…

There is a growing need for unbiased clustering methods, ideally automated. We have developed a topology-based analysis tool called Two-Tier Mapper (TTMap) to detect subgroups in global gene expression datasets and identify their…

In this work we deal with parameter estimation in a latent variable model, namely the multiple-hidden i.i.d. model, which is derived from multiple alignment algorithms. We first provide a rigorous formalism for the homology structure of k…

We characterize those ex-ante restrictions on the random utility model which lead to identification. We first identify a simple class of perturbations which transfer mass from a suitable pair of preferences to the pair formed by swapping…

We consider a distributed detection system with communication constraints, where several nodes are arranged in an arbitrary tree topology, under the assumption of conditionally independent observations. We propose a cyclic design procedure…

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…

Recently, there has been interest in extending long-known results about the multispecies coalescent tree to other models of gene trees. Results about the gene duplication and loss (GDL) tree have mathematical proofs, including species tree…

Frequent pattern mining is a relevant method to analyse structured data, like sequences, trees or graphs. It consists in identifying characteristic substructures of a dataset. This paper deals with a new type of patterns for tree data:…