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Each dataset contains 100 mutations grouped into 10 clones that accumulated following the infinite sites assumption.
Further information is not necessary, as the simulation works on a pseudoinfinite sites assumption.
As the mutations adhere to the infinite sites assumption, it follows that B is a perfect phylogeny matrix (Gusfield, 1991).
The infinite sites assumption of the ms model prevents multiple mutations at the same site from occurring.
The unbounded fitness is due to the infinite sites assumption, which allows genomes to accumulate ever-increasing numbers of beneficial mutations (as favored by selection).
Therefore, the use of the PP model implies little or no recombination in genomic segments and the 'infinitely many sites' assumption from population genetics.
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When calculated under the infinite-sites assumption, the Canadian and Chilean populations were more diverse than the older Norwegian population (0.08579, 0.06247 and 0.01809, respectively).
In addition, they go beyond the individual-based model in one aspect, as they do not make the infinite-sites assumption but allow for recurrent mutation at the focal locus (but still with at most two alleles).
Coalescent models can also be used to develop exact solutions for the AFS under the infinite-sites assumption, and these are particularly amenable for some models with multiple populations (Wakeley and Hey 1997).
We also make the simplifying assumption that the uptake of tracer is uniform within an injection site (assumption 7).
For example, for adaptor proteins that interact with different sites on a receptor, the virtual phosphorylation site assumption introduces a false competition.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com