This is similar to the neutral networks implemented by Koelle et al. [ 6], wherein most amino acid changes result in little decrease to cross-immunity between strains, but some changes result in large jumps in cross-immunity.
We classified the ω-lineages into three evolutionary categories: accelerated (more than 0.75 quartile), conserved (less than the 0.25 quartile) and neutral, and implemented association tests for each of the visual-coloration gene pairs.
The expected frequency spectrum for neutral loci was estimated using the standard neutral model as implemented by the ms coalescent simulation software package (Hudson 2002).
P-values were determined using coalescent simulations (10,000 runs) of a standard neutral model as implemented in DnaSP.
For each simulation replicate, we used neutral coalescent simulations implemented in MS (Hudson 2002) to obtain a starting population of 20,000 chromosomes (N e = 10,000 diploids).
Signal peptides and cleavage sites were predicted by the hidden Markov Model and the neutral network algorithm implemented in SignlP 4.0 program (Petersen et al., 2011).
An inventive immobilization process using expanded vermiculite containing numerous internal pores, and a magnesium potassium phosphate composite (MKPC) as a near-neutral binder were implemented to achieve the preferable environment for growth and survival of bacteria within the hardened mortars.
On the other hand, if ion-neutral collisions are implemented at the exobase, one would also expect that if the incoming proton flux is largest on dayside, the proton flux at the exobase will be still largest in that region, after particle backscattering.
So-called neutral white spaces were implemented at strategic level through the steering committee, and at operational level through many different PhD teams and masterclasses.
Further details about the model can be found in Appendix A. The ion-neutral chemical model is implemented into the hybrid code using a spherical grid similar to the grid used for the neutral collisions described above.
