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Hence, the phyletic distance between x and y equals the sum of split weights for all those splits in which x and y belong to separate components.
Here, the distance between two taxa in the tree is measured according to "phenetic distance," the length of the path (i.e., the sum of split weights) from one taxon to the other in the tree.
A total of 92 out of 212 splits are compatible with the NJ tree topology and their sum of split weight amounts to 96% of the total network; and thus, the NJ tree explains most of the split variability in the data.
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The insertion point minimizes the sum of the split contradictions.
The mean number of splits and the mean sum of lengths of splits between a sequence and the NSI/CCR5-tropic sequences on the tree are used as the score predictive of the coreceptor usage.
Thus, the sum of phase splits is used as a diagnostic tool to investigate where anisotropy within the lithosphere has the greatest impact of MT responses.
A better prediction performance is achieved with the use of the sum of lengths of splits that separate a sequence from these CCR5 sequences – TPR of 0.47 and 0.45 in NSI/SI and R5/X4 datasets respectively with the AUC of 0.74 and 0.76 respectively.
We selected the regions at which rearranged reads (split reads) consisted of at least 70% of total reads mapped on boundary regions (sum of canonical and split reads).
We then calculate the sum of the phase split for 8 periods from 640 to 7680 s, consistent with the period band over which stable MT responses with small errors were obtained (Sarafian et al. (2015) and Additional file 1: Figure S1).
Using the split decomposition method [ 42], the data were canonically decomposed into a sum of weakly compatible splits and represented in the form of a splits graph.
This metric is equal to the sum of the number of splits in one tree that are not present in the other, scaled by the total number of splits present across the two trees.
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