Related papers: Data Requirement for Phylogenetic Inference from M…

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…

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…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…

One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…

We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…

Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

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…

Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…

The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…

A rigorous methodology is proposed to study cell division data consisting in several observed genealogical trees of possibly different shapes. The procedure takes into account missing observations, data from different trees, as well as the…