Related papers: Analysis of Phylogeny Tracking Algorithms for Seri…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…
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,…
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.…
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…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
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…
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
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…
Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…