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The cut off value for divergence from Hardy-Weinberg equilibrium was (p ≥ 0.001).
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The method for the evaluation of critical values for divergence and flutter of the nonconservative systems is briefly introduced in case of considering and neglecting damping effects.
Besides the obvious extreme values for divergence stated above, there is a more subtle but clearly visible decline in divergence from the first few positions towards the end of the reads, in general, divergence is higher for early position's distributions than for later ones.
The median values for divergence and wobble were 0.66%/hour and 10.8% respectively.
To estimate divergence times among lineages we used a coalescence approach that uses Bayesian inference and MCMC simulations to generate posterior probability values for divergence times as implemented in the program Beast[ 68].
Maximum parsimony yielded a very similar range of T e values for divergence of animals (473 - 691 Mya) when chicken calibration point was not used for time estimates (Additional file 1).
The value obtained for divergence time was converted to time in years using the formula t = t/u, where t is time in years, t is scaled divergence time and u is the mutation rate per site multiplied by sequence length.
The PCR success rates obtained in our experimental validation varied from 7 to 40%, accurately corroborating the PCR efficiency values expected for divergence time greater than 200 Million years [38].
The reported value of divergence for this allele is considered highly significant and lays within the top 5% of FST among all SNPs genotyped in the HapMap project [8], [14] [16].
Simulations found that 100,000 chains were sufficient for convergence and the starting value of divergence time for the Markov chain (T) was obtained using a standard HKA test for the reference genes, implemented in DnaSP.
Values of divergence for nodes within the C. olivieri complex were comprised between 6.6 and 9.5%.
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