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Demographic history of the haplogroups and the whole dataset was determined with different methods.
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The best fitting substitution models for each dataset were determined with the Akaike Information Criterion AICC) using ModelTest 3.06 [ 87].
For each gene, the likelihood of estimated Bayesian phylogeny (gene) and corresponding ideal species tree (ideal) to fit the dataset were determined with the SH test at a 5% significance level.
Now, additional seven small RNA transcriptome datasets were used and target sites for all nine datasets were determined with the TAIR8 genome release [ 25].
The overall ML tree topology for each gene and the concatenated dataset was determined using GarliV0.951 [61] with model parameters as estimated by Modeltest.
Significant overrepresentation of particular GO terms in the dataset was determined using the software GeneMerge with corrections for multiple tests [50].
The statistical significance of the correlation of the proportion of each LH group at each GOS station with surface chlorophyll concentration (downloaded from the GOS dataset) was determined by Pearson's correlation on each dataset.
The dataset was originally prepared using the following criteria: all the structures in this dataset were determined using X-ray crystallography with resolution ≤2.0 Å, R-factor ≤0.25 and R-free factor ≤0.25; sequence length should be greater than 60 amino acid residues and without any chain breaks; each two sequences have sequence identity less than 30%.
Promoter regions (-1,000 to +200) of more than 70% of genes in the total dataset were determined by aligning full-length cDNA with corresponding genomic loci.
Glucose was determined with glucose oxidase.
Cell viability was determined with trypan blue.
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