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It is widely known, for instance, that support values such as the bootstrap proportion or posterior probability can strongly support an incorrect split in a tree due to model violations or multiple phylogenetic histories within a data set [ 68].
LOMETS identified the top template from 2 × 0cA, which has the same architecture to the target but with domains containing swapped segments (Szilagyi et al., 2012) (Supplementary Fig. S1B); this results in an incorrect split (1 98) (99–162) (163–241) (242–311) by ThreaDom (Supplementary Fig. S1C).
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FastTree was less effective than PhyML in distinguishing correct from incorrect
MR rarely finds more incorrect splits than MRP.
In contrast, MRg and find up to 1.9% more incorrect splits, while MR and find up to 0.8% more incorrect splits.
MRg might miss less splits than MR, however it also finds more incorrect splits.
Both the percentage of missing splits (7.1% with MR compared to 8.6% with MRP) and of incorrect splits (3% compared to 4.3%) improves.
Reconstructing incorrect splits which give rise to false conclusions is obviously a more serious problem compared to the exclusion of some splits.
MR and do not find more incorrect splits on average for p nni = 0.1, and 0.1% more for p nni = 0.2.
With incompatible input trees, the results for MR are best, especially when both missing and incorrect splits are taken into account.
The increased proportion of genome alignments without a spanning intron (single exon transcripts) observed in An. albimanus could result from incorrect splitting of the transcript during the assembly of transcriptional units having more than one exon.
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