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The Asplenium DArT marker data set suggests that serpentine was the ancestral substrate of A. viride with two independent colonizations onto limestone (Figure 3).
To compare the power of haplotypes and single SNPs in finding QTL, we simulated QTL at known genetic locations using 100 evenly distributed SNPs removed from the marker data set.
The model described here assumes a full marker data set, but it can be readily modified to consider missing marker data based on a hidden Markov model as advocated by Jiang and Zeng [48].
After editing, the final marker data set included 492 057 SNPs for 5214 bulls.
This complete marker data set was employed for linkage analysis using Joinmap ver. 4.0.
We focused on LD between SNPs from the 90 k marker data set and those from the 9 k marker data set that were most closely linked to them.
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STRUCTURE provides a model-based Bayesian approach to explain population structure by using our entire AFLP markers data set to identify K clusters to which the program then assigns each individual.
Verbruggen et al. [ 51], in their recent research on the data requirements for resolving the red algal tree of life, indicated that up to 2.8 × 105 nucleotides of sequence data may be required to resolve some regions of the phylogeny, which is orders of magnitude more data than that provided by our concatenated three-marker data set.
Table 5 shows the percent of alleles captured by subsets of 20, 30, 40, and 50 for the various marker data sets.
This model can also be used to analyse DArT marker data sets due to the underlying assumptions for the restriction sites model, non-observable absence data for example, fitting the structure of DArT data.
These marker data sets are provided in File S1.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

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