Sentence examples for model the branch from inspiring English sources

In this model the branch of interest (foreground) can have sites with an ω-value larger than one and all other branches (background) are restricted to ω-values below or equal to one [69].

Since the trees used in our study are constructed using the "no-clock" model, the branch lengths serve as estimates of genetic distance and not time.

In the subsequent analyses using the branch-site model, the branch lengths and the transition/transversion rate ratio κ were fixed to their estimates under the M0 model.

For testing the MA model, the branch between the node corresponding to the duplication between Pg11 and Pg3 and the node corresponding to the duplication between Pg11a and Pg11c (i.e. the ancestral Pg11 gene) was considered as the late branch.

Using the free-ratio model, the branch leading to the Gallus genus was determined to have a high ω value (0.92) (Additional file 4), though this cannot be taken as strict evidence of positive selection.

Fractal geometry has been used to model the branching patterns of the hyphae of various Armillaria species.

The alternative hypothesis is that these two rates are unequal (r C ≠ r C ). Parameter estimation and likelihood computation was performed using the phyloFit program (Siepel and Haussler 2004), holding fixed all other parameters of the neutral model (the branch-length proportions, equilibrium frequencies, and substitution rate matrix).

Under the MC model, the branches have the same length (1 1 ratio) because the divergence time from the common ancestor is obviously the same for both sister genomes.

According to the free-ratio model, the branches within the cichlid clade evolved with at least as twice as large d N/d S (0.1269 0.1607) compared with the branch at the base of the clade (0.0687) (fig. 2).

To test the hypothesis of positive selection in soybean expansin genes, we used the site model and the branch site model in the CODEML program of the PAML v4.4 software package [ 67].

In this model, the foreground branches are the branches tested for positive selection, and the background branches are all other branches on the tree [ 48].