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First we present a unified description of such problems and discuss the reasons why simple naı̈ve methods cannot give satisfactory results.
For distant genomes, the original median-based parsimony methods cannot give result in reasonable time and we can expect that the result of parsimony method will not exceed the optimal result achieved by fixing part of the correct adjacencies.
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Note again that the LMIs method cannot give a solution: the number of vertices equals 225.
The proposed methodology is illustrated by a realistic numerical example for which the finite element method cannot give correct results.
However, X-ray photoelectron spectroscopy (XPS) method cannot give any information concerning the forms of desorbing species.
In some cases the Baumgarte method and HHT-α method cannot give reasonable results while the TLISMNI methods perform well when the contact and constraint problems are involved.
The results showed that the MSM distance outperforms the other three distances and the CV Tree method cannot give good phylogenetic topology for the 62 α-proteobacteria.
The FIM method cannot give any information on the interactions among these variables; however, it can be used to identify possible confounding chemicals/diseases even if the data set does not include any co-occurring measures.
Testing the modified DL method on the data sets used in previous studies [ 33, 34, 40], we found that this method can give very good phylogenetic topologies [ 41], while the CV tree method cannot give good phylogenetic topology for the 62 α-proteobacteria [ 40].
However, the methods we applied cannot give any information on how far the cytoplasmic pendrin is altered by sequence, conformation and function or if cofactors for trafficking the molecule are affected.
Thus, direct methods, either edge detection algorithms or region segmentations, cannot give satisfactory results for cell-shape analysis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com