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