Maximum number of iterations (-L) was set to 500 to prevent overly long runtimes for some inflation values.
Subsequently, it effects also the sensitivity, specificity, total count of clusters and count of orphan clusters (i.e. clusters with only one member), which are shown in Figure 1 for different inflation values.
Collinearity was assessed by examining the tolerance values and variance inflation values for the independent variables in the final regression models; values < 0.1 and > 5, respectively, were considered to suggest problematic collinearity [ 17] (no problems with collinearity were found within the analyses carried out).
The optimal inflation value for TRIBE-MCL was 2.6 for the ABC transporter genes instead of 1.2 for the chemosensory genes, because lower inflation values cause TRIBE-MCL to incorrectly cluster the more conserved ABC transporter genes into fewer and bigger clusters.
Adjusted for inflation, land values in New York City leapt by more than 50% in the 1920s, buoyed by high rents and new high-rise technology that boosted the earning potential of a single property.
ESTs passing quality tests were clustered using the TribeMCL software (1E-50 and 95% identity for Blast alignment; inflation value 5; [ 65], and consensus contig sequences were generated using Cap3 [ 66]. For functional annotation we used the Gene Ontology annotation from the NCBI Gene database (Maglott et al., 2005).
Parameters were adjusted to a desired step size of 3 and cluster size between 40 and 400 for HCCA and an inflation value of 1.2 for MCL using Python 2.7.3 (http://www.python.org) and MCL version 12 068 (http://micans.org/mcl/), respectively.
With interest and adjustments for inflation, the value of the hoard has surpassed $50 million.
But when adjusted for inflation, the value of the remittances is actually expected to decline.
In contrast, for ABC transporter gene families, the optimal tree cut-off value for MC-UPGMA is at E-value 1e-14, and the optimal inflation value for TRIBE-MCL is 2.6.
