Related papers: Persistent Phylogeny: A Galled-Tree and Integer Li…
This paper characterizes and discusses devolutionary genetic algorithms and evaluates their performances in solving the minimum labeling Steiner tree (MLST) problem. We define devolutionary algorithms as the process of reaching a feasible…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
The social and economic importance of large bodies of programs and data that are potentially long-lived has attracted much attention in the commercial and research communities. Here we concentrate on a set of methodologies and technologies…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
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…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
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…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…