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(1) Population stratification, which was attributable to co-occurrence of molecular forms (M and S), and cryptic within-form stratification necessitating both a partitioned analysis and genomic control.
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For the Cameroon data, despite the application of a huge value of λ (31.78) stratification could not be removed from the data by GC (Figure 3a) and to avoid both false positives and negatives (Figure 3c) a partitioned analysis of M and S was essential.
A partitioned analysis was performed treating the cytb and 'Brown region' as separate partitions, each with their own DNA substitution models.
For the mtDNA analyses, a partitioned analysis was performed treating the cytb and cox2 genes as separate partitions, each with their own DNA substitution models.
A partitioned analysis (using the closest approximations in BEAST of the models applied in ML and BA, Table 3) never reached stationarity.
We assessed two possible methods of correction for stratification: a partitioned analysis (M and S analysed separately in Cameroon; and simply exclusion of M forms from Ghana owing to their rarity), and statistical correction of molecular form-related stratification by GC.
We also performed a partitioned analysis allowing different models for the three genomes.
A partitioned analysis was performed by concatenating 76 protein coding sequences from each full plastome.
However, we did not use a partitioned analysis within RAxML, thus somewhat hampering the accuracy of the maximum likelihood analyses.
In a partitioned analysis the model parameters (in this case, I and G) are calculated separately for each partition.
In this way, incongruence of a particular class of genes (such as transcription factors) in a partitioned analysis allow us to establish hypotheses about the evolution and potential function of these gene classes.
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