This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …

Gene sequences contain a gold mine of phylogenetic information. But unfortunately for
taxonomists this information does not only tell the story of the species from which it was …

Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease
challenge. These strains can accumulate many antibiotic resistance genes though …

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene
duplication, horizontal gene transfer and gene loss, and inferring these events in the …

The evolutionary history of a set of species is usually described by a rooted phylogenetic
tree. Although it is generally undisputed that bifurcating speciation events and descent with …

Gene phylogenies provide a rich source of information about the way evolution shapes
genomes, populations, and phenotypes. In addition to substitutions, evolutionary events …

The timing of the evolution of microbial life has largely remained elusive due to the scarcity
of prokaryotic fossil record and the confounding effects of the exchange of genes among …

A gene tree-species tree reconciliation explains the evolution of a gene tree within the
species tree given a model of gene-family evolution. We describe ecceTERA, a program that …

Abstract Summary RANGER-DTL 2.0 is a software program for inferring gene family
evolution using Duplication-Transfer-Loss reconciliation. This new software is highly …

Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many
important applications. However, sequence data alone often lack enough information to …