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The contamination was selected using a rating matrix, which assessed the contamination probability during the production process.
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The authors use a rate matrix derived from the Dayhoff model [ 43], and we adopt that as the default.
Here, such deviations are a consequence of using a single rate matrix to analyze sequences that were derived from two or three different ones.
Maximum-likelihood trees were generated with PhyML [ 20] using a WAG rate matrix with estimated invariant and gamma models, and reproduced to 100 bootstraps.
Specifically, we use the rating matrix to establish connections between a privacy-aware smart city and k-coRating, a novel privacy-preserving rating data publishing model.
The degree of correlation was explored using a correlation matrix for catch rate for all insects.
Using a transition matrix with unequal rates for ancestral state estimation, we sampled 100 character histories per tree.
The number string in the model name indicates the number of parameters optimized for the substitution rate matrix, and the remaining strings denote a rate matrix or a selective constraint matrix used.
Nevertheless, we are able to bound the difference between the convergence rate achieved using the optimal matrix, and the convergence rate resulting using a practically feasible matrix design.
MIGRATE-N estimated past migration rates among populations using a matrix model of asymmetric migration rates.
Most common models are defined using rate matrices, which are 4×4 matrices whose off-diagonal elements are non-negative substitution rates, and whose rows sum to 0. A stochastic transition matrix P is obtained from a rate matrix R through matrix exponentiation: P= e R. A common assumption made on the substitution process is that it is homogeneous throughout time.
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CEO of Professional Science Editing for Scientists @ prosciediting.com