After applying a site-specific rate model, these authors retrieved a phylogenetic tree of mammals that was in accordance with recent nuclear DNA based phylogenies [ 35].
To test the above possibility, we then reassessed the affinity between L. chlorophorum and P. minor by applying a site-heterogeneous substitution model claimed to be robust against long-branch attraction artifacts (Lartillot et al. 2007; Rodriguez-Ezpeleta et al. 2007).
In order to avoid an error caused by the local velocity structure when making the back-projection image, we applied a site correction to the arrival times.
For one out of three endonucleases applied, a site × depth interaction on T-RF richness (S) and Shannon's diversity index (H′) was observed, indicating differences between sites in the upper soil layer and depth effects on S and H′ for the extensively managed, low fertility site.
We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model.
To examine if any particular codons of CPGs of N. bombycis have undergone positive selection, we applied a site model approach with maximum likelihood using the software PAML (see Materials and Methods for details).
We applied a site-to-site variation model with two independent gamma distributions and the MG94 model, and tested for relevant internal branches in the tree.
To determine the influence of imperfect detection, i.e. false negatives, on PCR prevalence estimates, we applied a site-occupancy modeling framework to the dataset (Mackenzie et al. 2002, 2006).
In order to investigate whether directional (positive) selection might have affected the tree reconstruction, a ML analysis applying a branch-site model of evolution as implemented in PAML was performed.
Applying a single binding site fit a KD = 0.062±0.007 mM for NADH was determined.
This study applies a Total Site Heat Integration approach in conjunction with a detailed process and utility model, to develop an innovative ultra-low energy milk powder plant design.
