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Table 2 Parameter estimates and likelihood scores for branch-site model, model B.

From: The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

Model P L Estimates of parameters Positively selected sites
MPO
Model B
5 -33655.0405 p0 = 0.4975, p1 = 0.4553, (p2 = 0.0246, p3 = 0.0225)
Background:
ω0 = 0.0458, ω1 = 0.3307, ω2 = 0.0458, ω3 = 0.3307
Foreground:
ω0 = 0.0458, ω1 = 0.3307, ω2 = 251.6783, ω3 = 251.6783
Foreground:
NEB
19 > 0.50
2 > 0.95
1 > 0.99
EPO
Model B
5 -33647.5634 p0 = 0.4967 p1 = 0.4469, (p2 = 0.0297, p3 = 0.0267)
Background:
ω0 = 0.0464, ω1 = 0.3322, ω2 = 0.0464, ω3 = 0.3322
Foreground:
ω0 = 0.0464, ω1 = 0.3322, ω2 = 774.6323, ω3 = 774.6323
Foreground:
NEB
28 > 0.50
6 > 0.95
4 > 0.99
LPO
Model B
5 -33627.3508 p0 = 0.4431, p1 = 0.3884, (p2 = 0.0898, p3 = 0.0787)
Background:
ω0 = 0.0470, ω1 = 0.3414, ω2 = 0.0470, ω3 = 0.3414
Foreground:
ω0 = 0.0470, ω1 = 0.3414, ω2 = 82.8559, ω3 = 82.8559
Foreground:
NEB
96 > 0.50
18 > 0.95
11 > 0.99
TPO
Model B
5 -33639.5793 p0 = 0.4358, p1 = 0.3690, (p2 = 0.1057, p3 = 0.0895)
Background:
ω0 = 0.0479, ω1 = 0.3468, ω2 = 0.0479, ω3 = 0.3468
Foreground:
ω0 = 0.0479, ω1 = 0.3468, ω2 = 999.0000, ω3 = 999.0000
Foreground:
NEB
82 > 0.50
8 > 0.95
  1. Model B allows each foreground lineage to be tested independently of all other lineages, hence the four clusters (MPO, EPO, LPO, TPO – each in turn treated as foreground), and estimates 5 parameters (P) in total. p0, p1, p2 and p3 are proportions of sites in the dataset with the corresponding ω value, i.e, ω0, ω1, ω2 and ω3 for the foreground and the background lineages independently. The final column gives the estimated number of sites with posterior probabilities of greater than 0.50 of belonging to the positively selected category. Note: NEB: Naïve Empirical Bayes analysis.