Most phylogenetic trees are inferred using time-reversible evolutionary models that assume
that the relative rates of substitution for any given pair of nucleotides are the same …

Background The vast majority of phylogenetic trees are inferred from molecular sequence
data (nucleotides or amino acids) using time-reversible evolutionary models which assume …

Amino acid substitution models are a key component in phylogenetic analyses of protein
sequences. All commonly used amino acid models available to date are time-reversible, an …

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many
distance-based and character-based phylogeny inference methods. The procedure …

A phylogenetic tree is a diagram that illustrates the relationships between species or
organisms across time. Building phylogenetic trees is a crucial task in bioinformatics …

Background We compared two methods of rooting a phylogenetic tree: the stationary and
the nonstationary substitution processes. These methods do not require an outgroup …

Maximum likelihood estimation of phylogenetic trees from nucleotide sequences is
completely consistent when nucleotide substitution is governed by the general time …

Nonhomogeneous substitution models have been introduced for phylogenetic inference
when the substitution process is nonstationary, for example, when sequence composition …

We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species
tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale …

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that
the underlying evolutionary process was globally stationary, reversible, and homogeneous …