Sentence examples for using the gtr model from inspiring English sources

The ML and NJ trees were built using the GTR model, with a proportion of invariable sites and Γ-distributed Γ-distributedsites.

Maximum likelihood phylogenies were calculated on in-frame codon alignments with RAxML [54], using the GTR model with four gamma categories for rate heterogeneity (with parameters estimated from the alignment by RAxML).

Maximum likelihood trees obtained for each region using the GTR model of evolution showed a clear phylogenetic incongruence between the two derived region trees (Table S2 and File S1 in Supplementary material).

To estimate divergence times and molecular evolutionary rates, a Bayesian method implemented in MCMCTREE (in PAML [19]) was applied either with the CR model [12], [13] or with the IR model [15] (using the GTR model with a discrete gamma distribution with five rate categories (Γ5) for nucleotide substitutions), and multiple calibrations were incorporated through the time prior.

The neighbor joining tree was constructed using the GTR model and 1,000 bootstrap replicates.

We inferred phylogenetic trees for all the eight segments using the GTR model of evolution.

> -wrap-foot> When the strict clock model using the GTR substitution model was tested, the posterior distribution pattern of the mean age of the root of the tree was 19.91 Myr (95% HPD: 18.96 20.87) in Tricyrtis, and the root age of the outgroup (Calochortus) was 40.01 Myr (95% HPD: 39.0 41.0; Table  4).

NJ search and bootstrap analysis were carried out in PAUP using the GTR substitution model with 500 replicates.

A maximum likelihood consensus tree was calculated for the same dataset using MEGA v.5.05 [ 44], with 500 bootstraps and using the GTR substitution model.

So this method was run using the GTR substitution model on a neighbor-joining phylogenetic tree by the Datamonkey web server.

A phylogenetic tree was constructed based on binary data (CNVR present/absent) in MrBayes v.3.2 (Ronquist et al. 2012) using the GTR substitution model (Gatto et al. 2006).