Related papers: Data Requirement for Phylogenetic Inference from M…

Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…

Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…

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,…

Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…

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…

The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

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…

A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…

Terraces are potentially large sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The set of trees on a terrace can be…

Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…

In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…

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…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

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…