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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).