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To quantify variation in RF within and between populations we calculated the mean ± standard deviation (SD) and the coefficient of variation (CV = SD/mean × 100) of each population.
To identify those INDELs with high differentiation between populations, we calculated the minimal frequency differences of the derived alleles between all pairs of populations and took into consideration all differences ≥ 20%% (δ ≥ 0.2).
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To quantify mtDNA differentiation between species and/or populations we calculated the average and the net number of nucleotide substitutions per site (Dxy and Da, [ 50]).
To investigate the tissue specificity of genes expressed differently between sexes or populations, we calculated the statistic τ, which ranges from zero (housekeeping gene) to one (highly tissue-specific gene) (Yanai et al. 2005; Larracuente et al. 2008).
To compare patterns of W→S DAF skew between the three populations, we calculated pairwise correlations of U-norm in 40 kb and 1 Mb windows across the genome.
To examine the potential role of selection in driving the marked genetic differentiation between highland and lowland populations, we calculated F ST values per locus between Le Maido (2,062 m) and St. Leu (509 m) on the east side of the island.
To investigate if SES explained the differences in incidence rates of SAB between non-Indigenous and Indigenous populations we calculated age standardized incidence rates stratified by IRSAD quintiles.
To inspect overall patterns of genetic differentiation between the RG and FR populations, we calculated F ST [abbreviated here as F; see Eq. (1) in Materials and Methods], as defined by Weir and Cockerham (1984), using the estimator of Hudson et al. (1992).
To compare the frequencies of SNPs associated with phenotypes and disease between Turkish population and other world populations, we calculated the frequencies of SNPs listed in the GWAS Catalog [ 53] among world populations using data from 1000 Genomes Project [ 2].
To estimate correlations between eyespot characters in the base population, we calculated Pearson product-moment correlations between the target eyespots in the starting population for each experiment.
For each pairwise comparison between populations, we first calculated the percentage of the number of localities of Ensatina that were associated with the vegetation classes unique to either of the two focal populations.
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