Sentence examples for mutation rate matrix from inspiring English sources

This model does not assume a constant instantaneous mutation rate matrix over the tree and, therefore, trees evolving under this model are time nonhomogeneous.

We represent the codon mutation rate matrix M as follows by assuming that nucleotide mutations occur independently of codon positions but multiple nucleotide changes can infinitesimally occur.

The full model outperforms both models assuming strand symmetry, i.e. where mutation rates from nucleotide i to j is equal the mutation rates from j to i or models assuming the same mutation rate matrix in all lineages (Table 3).

In the present model, a nucleotide mutation rate matrix is fully parameterized by 8 parameters, and one additional parameter (m) is employed to represent the ratio of multiple to single nucleotide changes in a codon.

They allow for varying phylogenies and evolutionary parameters along the sequence by assuming that changepoints occur along the alignment and within each section there is a separate phylogeny and mutation rate matrix.

For example, many of them rely on continuous-time Markov processes with a constant instantaneous mutation rate matrix along the tree (the so-called global homogeneity), and also assume time-reversibility (and hence stationarity).

A structure imposed on such models assumes an instantaneous a→b tuple mutation rate expressible as a symmetric matrix on a and b, multiplied by a factor dependent upon the equilibrium frequency distribution of either the resulting tuple (b) or the resulting nucleotide in the mutation that occurs.

To carry out the optimization procedure, the GA parameters population size (pop), crossover rate ((p_mathrm{c})), mutation rate ((p_mathrm{m})), genome length (l), and cluster center matrix (V) are initially set.

For each original sequence in the database, we added 5, 10, 20, 30 or 40 similar sequences by substituting residues with a mutation rate of 20%, based on the BLOSUM62 substitution matrix.

To obtain a fuller understanding of the dynamics of mutation rate evolution, the preceding formulations might be applied in a transition matrix approach for the various mutation rate classes, although in the absence of explicit information on the rates of origin of mutator/antimutator alleles, the issue is not pursued here.

The exhibited conservation of non-consensus nucleotides does not take place if the elements of mutation matrix are identical, and can be related to the reduced mutation rate between the non-consensus nucleotides.