BUSTED

Usage

BUSTED(submodel: Double -> CTMC<Codons<a>>, omegaDist: DiscreteDist<Double>, posP: Double, posW: Double, posSelection: Int, n: Int) → CTMC<Codons<a>>

Arguments

Underlined names in default expressions refer to other arguments. A default beginning with ~ specifies a prior distribution.

submodel:

The model as a function of dN/dS

Default: |w:GTR+>x3+>dNdS(omega=w)|

omegaDist:

The conserved omega (i.e. dN/dS) values

Default: ~DirichletMixture(Uniform(0,1), 2, n)

posP:

The fraction of positively selected sites

Default: ~Beta(1,10)

posW:

The dN/dS value for positively selected sites

Default: ~LogGamma(4,0.25)

posSelection:

The model selector: 1 if positive selection, 0 if not

Default: ~Bernoulli(0.5)

n:

The number of conserved omega categories, if not specified

Default: 2

Original default expressions
omegaDist 
~DirichletMixture(Uniform(0,1), 2, @n)

Description

A Bayesian test of positive selection using the BUSTED model. The BUSTED model constructs a weighted list of (n+1) dN/dS values and constructs rate matrices from them. The first n rate matrices are conserved, and the last rate matrix is positive selected with weight posP and dNdS=posW. Instead switching between these rate matrices using a covarion process, the BUSTED model simply lets each (branch,site) pair choose a rate matrix from the mixture.
The test for positive selection compares the unrestricted BUSTED model to a restricted version with posW=1. The posterior probability that posSelection=1 is the posterior probability of positive selection.
All branches are treated as 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.)

Examples

BUSTED +> ASRV.Gamma(n=3)                              // with synonymous rate variation (= BUSTED-S)
BUSTED +> ASRV.Free
|w: GTR +> MNM +> dNdS(omega=w)| +> BUSTED              // with multi-nucleotide mutations
|w: GTR +> x3 +> dNdS(omega=w) +> MutSel| +> BUSTED    // with mutation-selection-balance

Citation

Murrell, Ben; Weaver, Steven; Smith, Martin D.; Wertheim, Joel O.; Murrell, Sasha; Aylward, Anthony; Eren, Kemal; Pollner, Tristan; Martin, Darren P.; Smith, Davey M.; Scheffler, Konrad; Kosakovsky Pond, Sergei L. (2015). Gene-Wide Identification of Episodic Selection. Mol. Biol. Evol. 32(5): 1365--1371. Article

See also

BranchSiteMixture, BUSTED_S