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In the first step, the algorithm is begun by taking a maximum repeat value.
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Larger values for the Maximum Repeat Size parameter were tried, but no groups larger than ~600 bp were ever identified.
These steps are repeated until either the maximum loop value is met or the fitness function has converged.
However, to ensure the robustness of our results, we have repeated our analysis by also using both the maximum probe value and selecting one probe set at random given a choice of multiple probe sets.
This is repeated until the update rule does not hold or the maximum h value, h max, is reached.
Here, d2 is the squared difference in number of repeat units between the two alleles at a given locus, standardized by the maximum observed value at that locus, and averaged across all measured loci [see 46], [63], [70].
We repeated the random selection of 88 haplotypes 100 times and then found the average maximum LD value for each window pair.
The resulting list of genes was first filtered to avoid redundances, assigning the maximum β-value observed among repeated genes; secondly, by selecting genes with absolute │Δβ│ = │βTAF − βCF│> 0.2.
maximum fitted value.
maximum AST value.
Calculation of the maximum histogram value (Max H).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com