Related papers: Gene tree species tree reconciliation with gene co…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
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…
In this research, we investigate the possibility of applying a search strategy to genetic algorithms to explore the entire genetic tree structure. Several methods aid in performing tree searches; however, simpler algorithms such as…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…
Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…
In many applications of evolutionary algorithms the computational cost of applying operators and storing populations is comparable to the cost of fitness evaluation. Furthermore, by knowing what exactly has changed in an individual by an…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…