相关论文: Distances between Extension Spaces of Phylogenetic…

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…

Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…

Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…

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…

Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…

Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

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…

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…

Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…

Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…

Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…

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…