The archaeal domain is currently divided into two major phyla, the Euryarchaeota and
Crenarchaeota. During the past few years, diverse groups of uncultivated mesophilic …

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 …

Abstract IQ-TREE (http://www. iqtree. org, last accessed February 6, 2020) is a user-friendly
and widely used software package for phylogenetic inference using maximum likelihood …

INTRODUCTION Crocodilians and birds are the two extant clades of archosaurs, a group
that includes the extinct dinosaurs and pterosaurs. Fossils suggest that living crocodilians …

Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled
volumes of genome sequence data generated to study and help contain the COVID-19 …

Appropriate and extensive taxon sampling is one of the most important determinants of
accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary …

Understanding the emergence of novel viruses requires an accurate and comprehensive
annotation of their genomes. Overlap** genes (OLGs) are common in viruses and have …

In phylogenetic inference, we commonly use models of substitution which assume that
sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of …

Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary
lineages can be densely sampled. This permits better phylogenetic estimates and …

Substitution models of evolution describe the process of genetic variation through fixed
mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost …