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While the matching topologies of the 15-locus *BEAST analyses and all other methods using the complete dataset make us confident in the results from *BEAST here, we acknowledge that full coalescent analyses such as *BEAST should ideally include multiple individuals per terminal taxon, as this greatly improves all aspects of tree estimation [ 18].
We also ran these models two ways: using the complete dataset and using a dataset that excluded on-indication side effects, as in the previous enrichment analysis.
Polymorphisms in regions surrounding ethA (top left), thyA (top right), pncA (bottom left) and katG (bottom right) using the complete dataset (n = 6,465) The top panel shows the density of SNPs per kilobase (green, nonsynonymous; black, all).
Firstly, using the complete dataset for training, all the E. coli in this dataset are predicted as pathogenic.
Using the complete dataset, there was no evidence that nucleotide diversity is affected by longitude (F1,50 = 0.131, p = 0.719), and borderline evidence that it is affected by habitat type (F3,50 = 2.404, p = 0.078), but there is strong evidence that nucleotide diversity declines with increasing latitude (F1,50 = 8.334, p = 0.006).
Using the complete dataset, with 1,439 individuals and 315 described and undescribed species from Australia and neighboring areas, the number of clusters fully agrees with the number of a priori identified species at a sequence similarity threshold between 1 and 2% (Figure 2A).
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As previously explained, we restricted the sample to 124 observations (from a complete sample of 670 observations), although we will use the complete dataset to test the robustness of the results.
For the Sanger dataset, we used the complete dataset of 5 loci and subsets of 4 loci (removing CytB), 4 loci (removing COI), and 3 (nucDNA only) loci.
We used the complete dataset to infer the groEL phylogeny, identify groEL haplogroups (groups of related haplotypes), and examine the possibility of bidirectional CI.
In order to do this, we used the complete dataset as training set and determined λ and C via cross-validation as described in Section 3.1.
Therefore, first we used the complete dataset for pig global immune response and second only the data corresponding to PRRSV infection for the pig response to PRRSV which consisted of 6 datasets harbouring 279 chips.
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