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We suggest that as context dependent models are intended to measure departures from independence, they should conveniently include an independent monomer process.
Our focus has been on establishing how to measure departures from independence, and in particular the identification of primary influences in departure from independence in the evolution of DNA sequences.
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Fay and Wu measure departure from this expectation with their H statistic [ 14].
Beside bootstrapping, popular tools frequently used by systematists were for some time the estimation of consistency and of tree length distribution under the parsimony criterion [ 104- 108] and derived tests that measure departure from a model of randomness.
They are formulated as optimization problems, seeking values for the model's inputs that minimize a cost function measuring departures from steady state and from date.
With respect to the latter, one can estimate using a linkage disequilibrium method that measures departures from expected proportions (Weir and Hill 1980; Waples 1991; Bartely et al. 1992).
For each population, nuclear genetic polymorphism was described using measurements of allelic richness (A r ), genetic diversity (H e ) and the unbiased intra-population fixation index [ FIS, measuring departures from Hardy Weinberg (HW) equilibrium within populations] for each locus and over all loci using fstat version 2.9.3.2.
Contrast this with the NF form where NFnuGTR is the nucleotide GTR, NFdiGTR is always measuring departures from independence and the context rate parameters (e.g. CG ⇔ TG) in all NF models have, under the null of no effect, the expected value of 1 regardless of sequence composition.
The first discrepancy measures departure from association when the latter is true, and the other measures departure from independence when this attribute holds.
The FIS (table 3; column 4) measures departure from the Hardy Weinberg equilibrium.
Define parameters D ij = p ij − p i. p j., measuring departure from independence (i.e. disequilibrium between alleles i and j).
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CEO of Professional Science Editing for Scientists @ prosciediting.com