Sentence examples for model substitution from inspiring English sources

Proper mixing of chains, acceptance probabilities and convergence of likelihood values, tree topologies, branch lengths and model substitution parameters were checked in the four runs before the samples were pooled.

The amino acid model substitution used was JTT [ 29].

The best-fitting substitution model, substitution rate, and general parameter setting followed the phylogenetic reconstruction using BEAST described above.

Nuclear coding genes were treated as one partition (PROTCAT model, substitution matrix LG + F, taken from ProtTest [ 45]).

All other INDELible parameters were set to the following: "NUCLEOTIDE 2" model, substitution model: "HKY 2.5," and maximum indel length: 50.

Under this model, substitution rates are allowed to vary within a lineage and across lineages within the dataset under the constraints of a prior distribution.

The BDP does not model substitutions, thus, substitutions are superimposed onto the BDP, whereas PTP explicitly models substitutions.

In the simplest, the Jukes and Cantor (1969) (JC69) model, substitutions between different nucleotides are assumed to occur all at the same rate.

It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment.

Maximum likelihood (ML) methods provide the best estimates of evolutionary change and genetic difference by modelling substitutions.

Thus, in our model, condom substitution also affects such HIV-positive individuals making the effect of such substitution worse.