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 …

We review recent models to estimate phylogenetic trees under the multispecies coalescent.
Although the distinction between gene trees and species trees has come to the fore of …

RDP4 is the latest version of recombination detection program (RDP), a Windows computer
program that implements an extensive array of methods for detecting and visualising …

RDP3 is a new version of the RDP program for characterizing recombination events in DNA-
sequence alignments. Among other novelties, this version includes four new recombination …

T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the
reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal …

The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and
hypotheses on the key aspects of the evolution of life on earth in light of comparative …

Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic
DNA between organisms through a process decoupled from vertical inheritance. In the …

Background Phylogenies, ie, the evolutionary histories of groups of taxa, play a major role in
representing the interrelationships among biological entities. Many software tools for …

The branching order and coherence of the alphaproteobacterial orders have not been well
established, and not all studies have agreed that mitochondria arose from within the …

Background The concept of a tree of life is prevalent in the evolutionary literature. It stems
from attempting to obtain a grand unified natural system that reflects a recurrent process of …