Table 1

Summary of all simulation conditions

Model

G+C%

Initial # Sites

κ

α

Insertion/Deletion Rate

Mean Indel Size

True distances simulated

JC

0.5

1000

n/a

n/a

100/40

4

0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0

HKY

0.6

1000

3.6

n/a

100/40

4

0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0

HKY + Γ

0.6

1000

3.6

1.0

100/40

4

0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0

HKY

0.6

100

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

200

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

300

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

400

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

500

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

1500

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

2000

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

5000

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

10000

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.6

1000

3.6

n/a

100/40

2

0.5, 1.0

HKY

0.6

1000

3.6

n/a

100/40

6

0.5, 1.0

HKY

0.6

1000

3.6

n/a

100/40

8

0.5, 1.0

HKY

0.6

1000

3.6

n/a

100/40

10

0.5, 1.0

HKY

0.6

1000

3.6

n/a

200/80

4

0.5, 1.0

HKY

0.6

1000

3.6

n/a

150/60

4

0.5, 1.0

HKY

0.6

1000

3.6

n/a

75/30

4

0.5, 1.0

HKY

0.6

1000

3.6

n/a

50/20

4

0.5, 1.0

HKY

0.7

1000

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.8

1000

3.6

n/a

100/40

4

0.5, 1.0

HKY

0.9

1000

3.6

n/a

100/40

4

0.5, 1.0

HKY + Γ

0.6

1000

3.6

0.25

100/40

4

0.5, 1.0

HKY + Γ

0.6

1000

3.6

0.5

100/40

4

0.5, 1.0

κ is the transition/transversion bias. α is the shape parameter for Γ-distributed intersite rate variation. Insertion/Deletion Rate is relative to the point mutation rate, i.e., a rate of 100/40 indicates 1 insertion every 100 point mutations and 1 deletion every 40 point mutations. Each simulation condition was replicated 1000 times.

Rosenberg BMC Bioinformatics 2005 6:102   doi:10.1186/1471-2105-6-102