Table 1 Comparison of the NHML, (NH)PhyML and BppML programs. Likelihood: - log (likelihood) of the optimized parameters, with a fixed tree topology.
From: Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
Likelihood | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Rate | Constant | Γ(4) | Γ(4) + I | Covarion | ||||||||
Model | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 |
NHML | 15307 | 15034 | -- | 14145 | 13828 | -- | -- | -- | -- | 13750 | 13397 | -- |
PhyML | 15187 | 15011 | -- | 14141 | 13824 | -- | 14128 | -- | -- | -- | -- | -- |
BppML | 15187 | 14920 | 15109 | 14141 | 13821 | 14029 | 14128 | 13810 | 14018 | 13747 | 13399 | 13615 |
Time | ||||||||||||
Rate | Constant | Γ(4) | Γ(4) + I | Covarion | ||||||||
Model | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 |
NHML | 0:01:40 | 0:02:28 | -- | 0:03:07 | 00:02:13 | -- | -- | -- | -- | 0:19:24 | 0:19:09 | -- |
PhyML | 0:00:07 | 0:01:43 | -- | 0:00:34 | 00:02:29 | -- | 0:00:35 | -- | -- | -- | -- | -- |
BppML | 0:00:27 | 0:11:57 | 0:01:12 | 0:00:47 | 00:35:46 | 0:00:48 | 0:01:01 | 0:29:40 | 0:01:38 | 0:02:52 | 1:14:32 | 0:14:27 |
Memory | ||||||||||||
Rate | Constant | Γ(4) | Γ(4) + I | Covarion | ||||||||
Model | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 | H | NH1 | NH3 |
NHML | 16.38 | 20.48 | -- | 55.30 | 65.54 | -- | -- | -- | -- | 55.30 | 65.54 | -- |
PhyML | 10.24 | 28.67 | -- | 30.73 | 77.82 | -- | 30.72 | -- | -- | -- | -- | -- |
BppML | 08.19 | 08.19 | 08.19 | 14.34 | 14.34 | 14.34 | 14.34 | 16.38 | 16.38 | 12.29 | 14.34 | 12.29 |