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Maximum likelihood phylogenetic trees were obtained with PHYML 2.4.4 [94] using the previously determined models of nucleotide substitution for each genome region and sample, and support for the nodes were evaluated by bootstrapping with 1000 pseudorreplicates.
However, there are less data from this region and sample sizes are generally smaller so the estimates may be less robust than those from the East.
For each region and sample, the read density was calculated using the RPKM (reads per kilobase per million of mapped reads) [ 72], and the relative enrichment z-score was calculated using Pyicoteo [ 64].
Therefore, we chose a simple approach to detect association decay with distance in order to select a region to perform a further fine-mapping study including a more dense screening over the selected region and sample replication for which multiple testing correction may be required.
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The account was mainly academic in style; nevertheless it excited a writer who went to the region and sampled the mushroom.
Univariable analysis showed significant differences in seroprevalence by age category (Table 1, p<0.0005), and a significant relation with region and sampling season at the 85% confidence level (Table 2).
We identified this region and sampled it intensively based on the biogeographic history and patterns of genetic diversity of other co-distributed fauna.
Univariable analysis was performed by the Adjusted-Wald test, considering the effect of species, age, and location (region and sampling site levels) on the RVF seroprevalence observed.
Our study was carried out along an environmental gradient marked by regions and sample locations labeled Coast, Coast Range, Willamette Valley, and Cascades Mountains.
To test this idea within the context of Australian vineyards, we considered 44 landscapes from two regions, and sampled invertebrates in vineyards central to each landscape five times at monthly intervals using canopy sticky traps.
The most widely used platform for HLA typing, capillary electrophoresis-based Sanger sequencing technology, does not scale with the number of regions and samples required in complex study designs when compared to next-generation sequencing (NGS) platforms.
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