Sentence examples for using a gtr model from inspiring English sources

In addition, a Bayesian tree was calculated with MrBayes 3.1 [45] using a GTR model with invariable sites and rate heterogeneity.

RAxML was used to fit 1,000 bootstrapped tree topologies and optimize branch lengths using a GTR model [ 31, 32].

PhyML [ 19] was used for the generation of phylogenetic trees using a GTR model estimated gamma distribution and 4 substitution rate categories.

The final phylogenetic tree was inferred from manually refined Mesquite alignment of sequences using maximum likelihood implemented in PHYML using a GTR model with estimated values for the α parameter of the Γ distribution and the proportion of invariable sites.

Bayesian phylogenetic inference was carried out using a GTR model with gamma distribution and 8 rate categories per partition (all parameters unlinked) and rate multipliers to accommodate rate differences among partitions.

Similarly, sequence divergences between mouse and another mammal under neutrality, d4 and di, were calculated by baseml of PAML [ 34] using a GTR model with gamma distribution for site heterogeneity (model = 7; ncatG = 5).

The analysis used a GTR model with among site rate heterogeneity (gamma distribution with 8 categories).

Each search used a GTR model of nucleotide substitution with the gamma model of rate heterogeneity initiated from a complete random starting tree.

We used a GTR model of substitution with heterogeneity among sites and we allow for different rates among cytb, cox1, cox3 and the non-coding regions.

For 28S we used a GTR+G model; for COI we used a GTR model with separate rates for each codon position.

Maximum likelihood trees were constructed with Phyml v3.0 [ 60] using a GTR substitution model and visualized with Dendroscope [ 61].