Sentence examples for model rate heterogeneity from inspiring English sources

We partitioned this protein sub-dataset by codon positions (2 partitions: codon positions [1+2], 3) and unlinked the substitution model, rate heterogeneity and base frequencies across them.

With jModelTest [57] the GTR+I+Γ model of nucleotide substitution was inferred from this data set using the "Bayesian information criterion" (BIC) with 6 rate categories, the proportion of invariable sites p-inv = 0.75 and the shape parameter of the Γ distribution α = 0.52 to model rate heterogeneity among sites.

The mitochondrial alignment comprising solely protein-coding genes (mtDNA2) was partitioned into codon positions and the substitution model, rate heterogeneity and base frequencies were unlinked across codon positions.

The alignment was partitioned into codon positions, and the substitution model, rate heterogeneity and base frequencies were unlinked across codon positions.

Methods that model rate heterogeneity include auto-correlation of rates among lineages [ 20], and uncorrelated models that allow rates assigned to lineages to be drawn from an underlying probability distribution [ 21].

The coding regions were then further partitioned according to 1+2 and 3 codon positions and the substitution model, rate heterogeneity and base frequencies were unlinked across codon positions ((1+2), 3).

We used a General-time-reversible (GTR) nucleotide substitution model and modelled rate heterogeneity among sites using a discrete gamma distribution with 4 rate categories.

Yoder and Yang (2000) modelled rate heterogeneity among lineage (heterotachy) using local clock models, a method that was recently reinvestigated using modern Bayesian-based sampling methods [ 22].

The final codon alignment was partitioned into the three separate codon positions, and each partition was unlinked, that is, substitution model parameters, rate heterogeneity model and base frequency were free to vary across partitions.

Tree reconstruction option, uses user defined tree search procedure, clocklike branch lengths on, exact parameter estimates, "JTT" substitution model, mixed model of rate heterogeneity (1 invariable + 8 gamma rates).

A GTR substitution model and rate heterogeneity modeled with a Gamma distribution and a proportion of invariable sites was used, as suggested by jModeltest [ 43].