Table 2

Fitting the class frequency mixture model (JTT + cF + Γ) to 25 protein data sets.
Protein
 Taxa
 Sites
 w(ΠF)
 w(Π1)
 w(Π2)
 w(Π3)
 w(Π4)
 ΛlnL
Carboxyl_trans
 36
 212
 0.74
 0.11
 0.06
 0.00
 0.10
 67.16
CTP-synthetase
 65
 212
 0.28
 0.29
 0.13
 0.04
 0.24
 225.24
DNA topo IV
 49
 228
 0.58
 0.15
 0.05
 0.02
 0.21
 162.77
Filament
 36
 210
 0.81
 0.10
 0.00
 0.05
 0.05
 39.58
Glu_synth_NTN
 40
 253
 0.66
 0.13
 0.04
 0.01
 0.17
 76.31
HSP70
 34
 432
 0.65
 0.17
 0.02
 0.0002
 0.16
 136.71
ILVD_EDD
 51
 310
 0.65
 0.14
 0.06
 0.01
 0.14
 181.56
MCM
 40
 220
 0.65
 0.18
 0.03
 0.00
 0.14
 74.38
MreB
 32
 275
 0.52
 0.20
 0.07
 0.00
 0.22
 141.87
Poty_coat
 34
 212
 0.60
 0.17
 0.04
 0.02
 0.18
 125.57
SecA
 70
 203
 0.40
 0.24
 0.09
 0.08
 0.19
 217.82
Usher
 36
 317
 0.78
 0.10
 0.02
 0.004
 0.10
 76.11
HSP90
 54
 459
 0.37
 0.19
 0.05
 0.09
 0.30
 279.92
NuoF
 41
 405
 0.37
 0.20
 0.11
 0.04
 0.27
 186.40
Cpn60
 41
 466
 0.52
 0.19
 0.04
 0.03
 0.22
 257.04
MPP
 43
 203
 0.73
 0.13
 0.03
 0.00
 0.11
 74.82
α-tubulin
 54
 375
 0.46
 0.16
 0.04
 0.01
 0.33
 90.05
β-tubulin
 46
 382
 0.59
 0.15
 0.03
 0.02
 0.21
 69.84
Actin
 48
 363
 0.58
 0.12
 0.03
 0.02
 0.25
 41.50
EF-1α
 38
 361
 0.60
 0.15
 0.05
 0.00
 0.21
 104.78
EF-2
 37
 669
 0.52
 0.16
 0.06
 0.03
 0.22
 273.30
enolase
 60
 305
 0.63
 0.13
 0.06
 0.00
 0.19
 24.08
myoglobin
 80
 153
 0.59
 0.14
 0.06
 0.03
 0.17
 35.73
lipoprotein
 23
 762
 0.77
 0.10
 0.02
 0.01
 0.10
 70.70
lysozyme
 36
 127
 0.61
 0.12
 0.03
 0.02
 0.23
 18.23

ΛlnL is the likelihood difference between the cF mixture model and the single frequency model (JTT + F + Γ). The p-values associated with these differences, calculated from χ2 tests with 4 degrees of freedom, are very significant in all cases (p < 0.01). The actual p-values would be even smaller as the tests are conservative (see the main text for a discussion).

Wang et al. BMC Evolutionary Biology 2008 8:331   doi:10.1186/1471-2148-8-331