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Table 2 Fitting the class frequency mixture model (JTT + cF + Γ) to 25 protein data sets.

From: A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

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

  1. 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).