Sentence examples for model and gamma from inspiring English sources

16 Since given correct assumption of the shape of hazard rate over time a parametric model is always more efficient than other models, I use Generalized gamma model to test whether Exponential model, Weibull model, Gompertz model, Lognormal model, Loglogistic model, and gamma model are appropriate.

For each PhyML analysis, ProtTest [86] was used to determine the appropriate substitution model and gamma parameter.

The Neighbor joining (NJ) tree was obtained under the JTT model and gamma distribution using MEGA version 3 [ 40].

For the probability models, we first used MrBayes with GTR model and Gamma + Inv and examined the posterior parameter estimates.

Maximum likelihood-based phylogenetic analysis was performed by RAxML version 7.2.3 [ 45] assuming the WAG model and gamma distribution of substitution rates.

MrModelTest ver. 2.3 [ 36] was used to determine the appropriate DNA substitution model and gamma rate heterogeneity using the Akaike Information Criterion AICC).

Analysis was conducted by using a general time-reversible model and gamma-distributed sites with separate rates for the 3 codon positions under a relaxed lognormal clock model.

Except for the use of "Blosum62" as prior for the substitution model and gamma-distributed rate heterogeneity in the likelihood model (see above), default parameters were applied.

The phylogenetic trees were produced by the neighbor-joining (NJ) method [ 32] with the Jones-Taylor-Thornton (JTT) probability model and gamma-distributed (a = 1.0) rates among the sites were inferred by using MEGA4 software [ 33].

To test the robustness of the results to the distance calculation method, we produced a variant of the P1 data set distances that were estimated using the Protdist program of the PHYLIP package (Felsenstein 1996) with the Jones, Taylor, and Thorton evolutionary model and gamma-distributed site evolution rates with shape parameter of 1 (set P1").

Maximum Likelihood trees for the concatenated alignments (positions with >33% of gaps removed) of ribosomal proteins (6137 sites) and RNA polymerase subunits RpoA, RpoB, and RpoC (2625 sites) were constructed using TreeFinder [ 67], with the Whelan and Goldman [ 68] evolutionary model and gamma-distributed site rates.