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Analyses were based on the admixture ancestral model for a range of K values from 1 to 15.
Tight linkage of these neutral polymorphisms with more recently acquired low activity APS and HPS haplotypes does not satisfy a simple ancestral model and requires the development of a more complex population genetic model to account for pleiotropic selection.
We have analysed, in BAp, the distribution of the conserved specific target genes (using E. coli as the reference ancestral model) for the five NAPs (Additional file 3).
The data suggest that Tribolium may conserve more common miRNAs with other insects than with Drosophila and may therefore represent a more ancestral model of conserved miRNA function.
Overall, gene essentiality predictions using the iEntero_core ancestral model were in 80.3% (n = 325) agreement with at least one other data set from previously published data.
We compared the reactions retained in each ancestral model to the total set of reactions in the mature E. coli K-12 model for each reaction subsystem classification category.
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This work demonstrated a new approach for validation of carbon source utilization of ancestral models, yielding accuracies of >75%, for aerobic and anaerobic conditions for the ancestral core models for Ecoli/Shigella, E. coli/ Shigella/ Salmonella, and enterobacteria.
This supports the use of more general ancestral models in cases where a genome sequence, or specific model, or both are lacking.
This is a novel approach using quantitative ancestral models to study metabolic network evolution and may be useful for identification of new targets to control infectious diseases caused by enterobacteria.
It is also likely that we will see a reduction of orphan reactions in the next generation of ancestral models that makes use of parsimony or maximum likelihood based ancestral state prediction to determine which genes are present at each internal node, because this approach will be more tolerant of annotation or orthology errors affecting a subset of taxa.
Our results here provide additional support to the ancestral chromosome model, and hold promise for whole-genome comparative genome analysis.
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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.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com