Estimating the number of substitution events per site that have occurred during the evolution
of a pair of amino acid sequences is a common task in phylogenetics and comparative …

The pattern of substitutions at sites in proteins provides invaluable information about their
biophysical and functional importance and what selection pressures are acting at individual …

Background Accurately modeling the sequence substitution process is required for the
correct estimation of evolutionary parameters, be they phylogenetic relationships …

Amino acid substitution matrices describe the rates by which amino acids are replaced
during evolution. In contrast to nucleotide or codon models, amino acid substitution matrices …

One of the first steps in the analysis of aligned nucleotide or amino acid sequences typically
is the computation of the matrix of genetic distances (or evolutionary distances) between all …

Approximate methods for estimating the numbers of synonymous and nonsynonymous
substitutions between two DNA sequences involve three steps: counting of synonymous and …

In the field of molecular evolution, we commonly calculate site-specific evolutionary rates
from alignments of amino-acid sequences. For example, catalytic residues in enzymes and …

Current mathematical models of amino acid sequence evolution are often applied in variants
that match their expected amino acid frequencies to those observed in a data set under …

Analytical molecular distance estimates can be inaccurate and biased estimates of the total
number of substitutions not only when the model of evolution they are based on is incorrect …

The first step in the analysis of aligned nucleotide or amino-acid sequences usually consists
of the computation of genetic distances (or evolutionary distances) between the …