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Given that little is known about the robustness of these geometric arrangements, we undertook to characterize phyllotaxis by measuring divergence angles between organs along the stems of wild-type and specific mutant plants with obvious defects in phyllotaxis.
This is indeed what we observe in the form of a strong correlation between the number of alleles per site and its average negated phyloP score (Siepel et al. 2006) measuring divergence across vertebrates (Spearman's ρ = 0.52; P < 2.2 × 10−16).
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Intuitively, this can be understood by considering that polymorphisms can often be confused with fixed differences between species when single, or few, sequence comparisons are used to measure divergence.
The KL measures divergence between the root state prior and posterior probability for each MCC tree.
We measured divergence levels per site by estimating the Poisson amino acid distances for each amino acid site in the multiple sequence alignments.
The first time point in a clinical study is generally at a point that had already deviated from what can be called a 'healthy state,' whereas experimental studies usually measure divergence from the 'healthy state' under controlled conditions.
To infer patterns of substitution independently for each lineage, we measured divergence from a putative ancestral sequence inferred by maximum likelihood for the P. berghei P. yoelii and P. chabaudi-P.
For each previous study, we then noted where the reported differentially expressed genes were located in our sorted list, and assessed the resulting significance using a Z score to measure divergence from a random distribution.
We will use it to measure divergences to the "initial" and "final" transcriptomic states (two states of reference).
The beam size was 0.2 mm × 0.2 mm, and measured divergences were less than 0.0001 radians.
It should be stressed that the measured divergences between unionoid F and M genomes considerably surpass intra- or inter-species values reported in classical model systems used for the study of intergenomic co-evolution [ 9, 79, 80].
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