TABLE 1.

A representative sample of simulation results

Outgroup	Probe sets	t1	t2	log2(t1/t2)	a	σ	p
No	No	1.91 (1.72–2.08)	0.36 (0.27–0.52)	2.45 (1.83–2.75)	0.50 (0.48–0.54)	0.18 (0.12–0.18)	0.00 (0.00–0.01)
Yes	No	2.02 (1.86–2.16)	0.49 (0.43–0.56)	2.00 (1.83–2.24)	0.50 (0.47–0.53)	0.12 (0.10–0.14)	0.01 (0.01–0.01)
No	Yes	2.01 (1.39–2.40)	0.50 (0.37–0.64)	2.00 (1.49–2.51)	0.43 (0.33–0.49)	0.30 (0.22–0.35)	0.00 (0.00–0.00)
True parameters		2.00	0.50	2.00	0.50	0.10	0.01

Shown are medians and 25 and 75% quartiles for estimates of branch lengths t₁, t₂, and log₂(t₁/t₂) and shape parameters a, σ, and outlier proportion p over 20 simulated data sets with parameters close to values inferred from actual data (see Table 2). Inferences were made from data without (two-species tree) or with a single outgroup (three-species tree) and using either 1000 probes or 1000 probe sets, each consisting of a geometrically distributed number (mean 6) of identical probes. Full simulation results are presented in supplemental Tables 1–3.