Table 5

Simulation parameters used by PSPE for generating benchmark promoter sequences

Evolution distance per step

0.05 substitution per site

Length of root sequences

3,000 bp

Background sequence model

Markov order of third

Base frequencies

A = 0.258, C = 0.242, G = 0.242, T = 0.258

Substitution model

HKY85

Transition:transversion ratio

20:1

Rate heterogeneity

Gamma (1.0) + Iota (0.1)

Range of GC content

(0.45, 0.55)

Gap model

Negative binomial distribution (1, 0.5)

Huang et al. Genome Biology 2007 8:R225   doi:10.1186/gb-2007-8-10-r225