BranchSite — The branch-site test for positive selection
from Zhang et al. (2005)
Usage
BranchSite(submodel: Double
-> CTMC<Codons<a>>, fs: List<Double>, omegas: List<Double>, posP: Double, posW: Double, posSelection: Int, branchCats: IntMap<Int>) → DiscreteDist<CTMC<Codons<a>>>
Arguments
A default beginning with ~ specifies a prior
distribution.
-
submodel: -
The model, as a function of dN/dS
-
Default:
|w:GY94(omega=w)| -
fs: -
Class frequencies in the background model.
-
Default:
~SymmetricDirichlet(2,1) -
omegas: -
dN/dS ratios for the first n-1 classes in the background model.
-
Default:
~IID(1,Uniform(0,1)) -
posP: -
The fraction of sites switching to positive selection on the foreground branches.
-
Default:
~Beta(1,10) -
posW: -
The dN/dS ratio for positively selected sites on the foreground branches.
-
Default:
~LogGamma(4,0.25) -
posSelection: -
The model indicator: if 0, the sites only switch to neutrality on the foreground branches.
If 1 then sites may switch to dN/dS=posW.
-
Default:
~Bernoulli(0.5) -
branchCats -
Default: The branch categories in the current context
Original default expressions
-
branchCats -
get_state(branch_categories)
Description
The posterior probability that posSelection=1 is the posterior probability that some sites undergo positive selection on the foreground branches.
The posterior mean of PrPosSelection can provide a more accurate estimate of this probability than the posterior mean of posSelection. The statreport tool uses LogOddsPosSelection to report the corresponding posterior log odds accurately, even when the probability is extremely close to 0 or 1. (Do not average LogOddsPosSelection directly.)
Citation
Zhang, Jianzhi; Nielsen, Rasmus; Yang, Ziheng (2005). Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular biology and evolution 22(12): 2472--2479. DOI: 10.1093/molbev/msi237