Related papers: Leaping through tree space: continuous phylogeneti…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
In this paper, we propose DeepTree, a novel method for modeling trees based on learning developmental rules for branching structures instead of manually defining them. We call our deep neural model situated latent because its behavior is…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
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 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…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
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…
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…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
We study the inference of network archaeology in growing random geometric graphs. We consider the root finding problem for a random nearest neighbor tree in dimension $d \in \mathbb{N}$, generated by sequentially embedding vertices…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
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 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…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…