Finally, we evaluated the confidence on the estimates of r/m (measure of the weight of recombination on diversification relative to mutation) and ρ/θ (measure of the frequency of occurrence of recombination relative to mutation events) obtained for each data set.
Furthermore, we evaluated the confidence of the results by the number of data for each block.
After all the data were analyzed, we compared our results to the original results to evaluate the confidence of the automatically generated simulation.
To evaluate the confidence of the internal nodes, the rapid bootstrap method [ 53] was applied with 1000 replications.
We ran BWA with its default parameters and used the same mapping quality threshold (namely, 10) to evaluate the confidence of the alignment results.
To evaluate the confidence of each motif score s, we used randomly selected coding sequences as the null model to test the statistical significance.
To systematically evaluate the confidence of the resulting PPI data, traditional resin-based coIP was the most common method for data verification.
The MOID algorithm provides a p-value for each measurement and thus a metric to evaluate the confidence of each data point.
The site-wise log-likelihoods calculated by TREE-PUZZLE (with option-wsl) for each topology served to evaluate the confidence of the reconstruction using the Approximately-Unbiased test (AU-test) implemented in CONSEL [ 53, 54].
Several were used to check the automated genotype calling and the sample clustering: (i) the Call Rate is the number of SNP successfully genotyped for each sample; (ii) the GenTrain Score evaluates the confidence of the genotyping for one SNP on all samples.
In the future, we hope to develop automatic algorithms to scan differences in annotation between third-party databases, evaluate the confidence of the annotations, add a wiki-like annotation support system, allowing other groups to include their expertise in the database, as well as refine the interface in order to allow more complex queries.
