Related papers: Identifying a species tree subject to random later…
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
Diffusion processes on trees are commonly used in evolutionary biology to model the joint distribution of continuous traits, such as body mass, across species. Estimating the parameters of such processes from tip values presents challenges…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial progress in developing methods that estimate a species tree…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Suppose $G$ is a tree. Graham's "Tree Reconstruction Conjecture" states that $G$ is uniquely determined by the integer sequence $|G|$, $|L(G)|$, $|L(L(G))|$, $|L(L(L(G)))|$, $\ldots$, where $L(H)$ denotes the line graph of the graph $H$.…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
We present a novel hierarchical triplet loss (HTL) capable of automatically collecting informative training samples (triplets) via a defined hierarchical tree that encodes global context information. This allows us to cope with the main…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
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,…