The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria,
a defining event in the evolution of eukaryotic cells. As usually described, this theory posits …

Blood coagulation, skin-barrier formation, hardening of the fertilization envelope,
extracellular-matrix assembly and other important biological processes are dependent on …

Current methods struggle to reconstruct and visualize the genomic relationships of large
numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic …

Motivation: Increasing attention has been devoted to estimation of species-level
phylogenetic relationships under the coalescent model. However, existing methods either …

Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the
clade support of phylogenetic trees. However, with the rapidly growing amount of data, this …

Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

The increase in the number of large data sets and the complexity of current probabilistic
sequence evolution models necessitates fast and reliable phylogeny reconstruction …

Alignment quality may have as much impact on phylogenetic reconstruction as the
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB
program package comprises a variety of directly interacting software tools for sequence …

Phylogenetic inference from amino acid sequence data uses mainly empirical models of
amino acid replacement and is therefore dependent on those models. Two of the more …