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) |