Sentence examples for model rate variation from inspiring English sources
Mr.Bayes employed the JTT model of amino acid substitution assuming the presence of invariant sites and a gamma distribution approximated by four different rate categories to model rate variation between sites.
We used a Gamma distribution with four rate categories to model rate variation in all analyses.
A phylogenetic tree was created using FastTree version 2.1.4 (Price et al. 2010) with a GTR model and a gamma parameter to model rate variation across sites.
Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages.
The authors mistake "relaxed molecular clock" for "approximate molecular clock": approximate molecular clocks correspond to model rate variation over time (e.g. with autocorrelation).
We also include a separate HMM to model rate variation along the sequence since ignoring this can lead to spurious recombination detection (Husmeier and McGuire, 2002).
Importantly, modeling rate variation seemed to be an important component.
However, adding parameters for modeling rate variation to either of the two models increased the model likelihood tremendously.
Another striking feature was that once parameters for modeling rate variation had been incorporated into the model, unlinking topologies did not seem to have as pronounced effect on the model likelihood (Table 2), compared to the models without rate variation.
Maximum-likelihood parameters (amino acid frequencies, percent invariant sites, and α for modeling rate variation among sites) were estimated in TREEPUZZLE 5.0 [ 77] under a Jones-Taylor-Thornton (JTT [ 78]) substitution matrix with invariable + Γ (four category) distribution of rates.
In addition to allowing non-clock-like relationships among sequences related by a phylogeny, modeling rate variation among lineages in a gene tree also enable researchers to incorporate multiple calibration points that may not be consistent with a strict molecular clock.
