Table 1 PSPE parameters for simulating sequence evolution
Original ancestral sequences | Human non-coding region |
|---|---|
Sequence length | 500 bp |
Base frequencies | A = 0.215, C = 0.287, G = 0.285, T = 0.214 |
Substitution model | HKY85 |
Transition:transversion ratio | 20:1 |
Point substitution:InDel ratio | 10:1 |
InDel model | Geometric distribution (p = 0.5) |
Heterogeneity of substitution rate | Gamma (1.0) + Iota (0.1) |
Range of GC content | (45%, 70%) |
Evolution distance per step | 0.05 substitution per site |