As more complete genomes are sequenced, phylogenetic analysis is entering a new era—
that of phylogenomics. One branch of this expanding field aims to reconstruct the …

Comparative genomics, using computational and experimental methods, enables the
identification of a minimal set of genes that is necessary and sufficient for sustaining a …

Background For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria)
was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure …

The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA
hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the …

Motivation: A tool that simultaneously aligns multiple protein sequences, automatically
utilizes information about protein domains, and has a good compromise between speed and …

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 …

Abstract The Crp-Fnr regulators, named after the first two identified members, are DNA-
binding proteins which predominantly function as positive transcription factors, though roles …

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all
organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of …

Within animals, evolutionary transition toward herbivory is severely limited by the hostile
characteristics of plants. Arthropods have nonetheless counteracted many nutritional and …

Genome comparisons indicate that horizontal gene transfer and differential gene loss are
major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the …