Table 1 Starting equilibrium base frequencies and results for the simulations with either homogeneous or heterogeneous sequences (i.e., those with sites from single versus multiple categories, respectively).
From: Using equilibrium frequencies in models of sequence evolution
Categories |
| π C | π G | π T | Biasb | f c |
|
|---|---|---|---|---|---|---|---|
A | 0.10 | 0.40 | 0.30 | 0.20 | 0.154 | 0.50 ± 0.01 | 0.00 ± 0.01 |
B | 0.30 | 0.30 | 0.30 | 0.10 | 0.105 | 0.50 ± 0.01 | 0.00 ± 0.01 |
C | 0.30 | 0.20 | 0.20 | 0.30 | 0.029 | 0.50 ± 0.02 | 0.00 ± 0.03 |
D | 0.40 | 0.20 | 0.20 | 0.20 | 0.078 | 0.49 ± 0.01 | 0.01 ± 0.01 |
E | 0.20 | 0.40 | 0.20 | 0.20 | 0.078 | 0.51 ± 0.01 | -0.01 ± 0.02 |
F | 0.20 | 0.20 | 0.40 | 0.20 | 0.078 | 0.50 ± 0.02 | -0.01 ± 0.01 |
A+B | 0.20 | 0.35 | 0.30 | 0.15 | 0.074 | 0.43 ± 0.01 | -0.11 ± 0.02 |
A+C | 0.20 | 0.30 | 0.25 | 0.25 | 0.015 | 0.34 ± 0.03 | -0.16 ± 0.03 |
B+C | 0.30 | 0.25 | 0.25 | 0.20 | 0.015 | 0.24 ± 0.02 | -0.33 ± 0.03 |
A+B+Ce | 0.23 | 0.30 | 0.27 | 0.20 | 0.016 | 0.39 ± 0.04 | -0.13 ± 0.04 |
D+E+Fe | 0.27 | 0.27 | 0.27 | 0.20 | 0.010 | 0.68 ± 0.03 | 0.29 ± 0.04 |
- aExpected nucleotide distribution.
- bNucleotide bias, as information content measured in bits:
. - cMean ± twice the standard error of the estimate.
- df = 0:0 for these simulations with the HKY model. With f = 0:0, the HKY+gwF variant is reduced in these simulations to its more standard F81 based model.
- eThe heterogeneous sequences in these simulations were of length 9,999, rather than 10,000, since the latter is not a multiple of 3.
.