The simulated result indicate that the maximum calculation error of the global phase-shifting is 1.5%.
The maximum likelihood calculations of dn/ds were performed for a subset of 100 sequences for all branches and also for trunk and non-trunk branches separately as explained in the 3 rd paragraph of the Results section and shown in Table 1.
After measurement of the relative fluorescence intensity (channel F3/F1) for each sample, a proportional baseline adjustment for sample quantification was carried out by second derivative maximum calculation, and the amount of each mRNA transcript was expressed as a threshold cycle (ct) value.
Many of the subprime mortgages had been financed through the securitization market, where a wondrous financial alchemy enabled risky investments to be transformed into supposedly safe investments rated AAA by the bond rating agencies, whose calculations of maximum possible losses turned out to have been woefully low.
These phylogenetic analyses were chosen for their speed (calculations of maximum likelihood trees of 100 bootstrap samples per data set were too slow).
Approximate molecular positions can be determined, in combination with a variety of feature-enhancing low-pass and band-pass filters (Křížek et al., 2011; Izeddin et al., 2012), by detection of local maxima, non-maximum suppression or calculation of the centroid of connected components of segmented objects.
Extension rate distributions have been calculated in a twin screw mixer for Newtonian and non-Newtonian fluids because they strongly affect dispersion of bubbles and the maximum stable diameter estimated from calculations of the Capillary number.
Calculations of the maximum total length of the cell cycle depend on assumptions about covariance between the length of G2 and the length of M + G1 + S. If cells having a longer G2 are assumed to have a proportionally longer M + G1 + S, then the maximum length of the cell cycle for 95% or 100% of cells is given by equation 6.
We compared our dN/dS scores for P. falciparum/reichenowi divergence (Nei-Gojobori method with Jukes-Cantor correction) with those previously reported for the same 40 genes using maximum likelihood for calculation of dN/dS [ 18].
Alignment, reconstruction of the phylogeny by maximum likelihood (ML), calculation of the rate of synonymous substitutions per synonymous site (Ks) and analysis of the Kimura 2-parameters distance (K2p) [ 50] were performed only for full-length sequences with both TIRs and LTRs, using the package Mega5 [ 51].
