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Exact(4)
As we mentioned in Section 2.4, for two histograms using the same partitioning method, the similarity between these two histograms at different resolution levels will obey the inequality described in (4).
One unconstrained and six constrained analyses were done with RAxML (iMAC Pthreads-version [ 70, 71]) using the same partitioning scheme as above under the GTR + G + I model [ 72].
Using the same partitioning around medoids algorithm to separate each of these additional independent cohorts into two subgroups we were able to confirm the prognostic role of the immune response-module across a total of 469 ER- tumours.
2.0 [ 56]) using the same partitioning scheme and model assignments as the BI analysis (above) and using the default settings except for the following: searchreps = 5, numberofprecreductions = 20, treerejectionthreshold = 100.
Similar(56)
A score of 10 means that the target was predicted for that compound in each of the ten runs of the Parzen-Rosenblatt method, using the same partitions as for Table 1, and corresponds to dark blue shading.
One thousand nonparametric bootstrap replicates were performed in RAxML using the same partitions and models of sequence evolution with one search replicate per bootstrap replicate and a random starting tree; branch lengths and model parameters were optimized during the bootstrap analysis.
The Bayesian tree was reconstructed with MrBayes v3.2.2 using the same partitions and model as in the ML analysis.
The GTR + Γ model was used, and all parameters of the substation model were separately estimated using the same partitions as mentioned above.
Bayesian analysis was performed on the datasets with MrBayes Ver. 3.2.1 [ 67] using the same partitions and models as described above.
Using the same partitioned bins as described above, we also compared the recombination rate with the genomic double-strand break (DSB) map generated by Pan et al. [ 18] (using immunoprecipitation of Spo11-bound oligos in meiotic SK1 cells).
We used the same partitions as in the MrBayes analyses.
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