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

Open Data