The phrase "allow for rate" is not correct and lacks clarity in written English.
It may be intended to express the idea of accommodating or considering a specific rate in a context, but it needs additional context to be meaningful.
Example: "We need to allow for rate fluctuations when budgeting for the project."
Alternatives: "account for rate" or "consider the rate".
The other two methods allow for rate variation among branches.
In this paper we have included models that allow for rate variation across the sequence and across the phylogeny.
TREE-PUZZLE 5.2 incorporates the JTT matrix for amino acid substitutions and gamma-distributed rates to allow for rate heterogeneity among sites.
In addition, the proportion of invariable sites and a gamma distribution parameter to allow for rate heterogeneity among sites (six categories) and uniform prior probabilities and tree topologies were implemented in the analyses.
We employed a Yule tree prior with uncorrelated lognormal relaxed clocks that allow for rate heterogeneity among lineages and used the same prior scheme for the global substitution rate of the mtDNA described above to calibrate divergence time estimates.
Our analysis used the Bayesian skyline model of population growth as a flexible demographic prior and the relaxed lognormal molecular clock to allow for rate variation among branches of the tree.
The plan will be financed by state revenue bonds, but allows for rate increases for consumers who use 30percentt more than a base amount of electricity set by region and climate.
More sophisticated metering and communications technologies are now economically feasible for many more customers, allowing for rate designs that provide improved economic efficiency, transparency, simplicity and fairness, and allow customers to make efficient energy choices.
Rather, it adjusts all rates for a site by a multiplier that allows for rate heterogeneity.
Furthermore, the analyses revealed no support for the gamma model, which allows for rate variation over the base model without gamma (Table 2).
The small magnitude of increase is probably why Bayes factors did not support either the partitioned model or the gamma model, both of which allowed for rate variation.
