Proportion of sites under positive selection detected | Parameters in the ω-distribution | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|

Family | No. of sequences in the analysis | Average
d_{N}/d_{S} | Tree length (CODEML) | P-value
M3:M0 | P-value
M3:M1 | P-value
M8:M7 | With M3 (%) | With M8 (%) | Model best fitting the data | ln L for
the
model
fitting
the best | M3 model | M8 model |

avrA | 3 | 0.2348 | 3.33406 | 1.09E-05 | 4.2E-06 | 7.94E-01 | NP | NP | M3 | −2749.29 | p0 = 0.34653
p1 = 0.23706
(p2 = 0.41641)
ω0 = 0.05365
ω1 = 0.05365
ω2 = 0.48857 | p0 = 0.59405
p = 6.07760
q = 99.00000
(p1 = 0.40595)
ω = 0.49497 |

avrB | 5 | 0.1758 | 29.93223 | 1.62E-23 | 3.6E-44 | 4.49E-02 | NP | NP | M8 | −3573.96 | p0 = 0.31227
p1 = 0.39459
(p2 = 0.29314)
ω0 = 0.00834
ω1 = 0.06173
ω2 = 0.50765 | p0 = 0.69727
p = 0.32013
q = 0.95376
(p1 = 0.30273)
ω = 0.03425 |

avrD | 10 | 0.5905 | 0.42266 | NA | 9.4E-01 | 7.43E-01 | 0.40 | 0.40 | M0 | −2109.60 | p0 = 0.25498
p1 = 0.74069
(p2 = 0.00432)
ω0 = 0.00001
ω1 = 0.80099
ω2 = 20.31307 | p0 = 0.99594
p = 0.42952
q = 0.28467
(p1 = 0.00406)
ω = 20.39960 |

avrF | 7 | 0.1617 | 9.1427 | 6.64E-10 | 7.0E-21 | 6.34E-01 | NP | NP | M3 | −1696.30 | p0 = 0.34049
p1 = 0.54809
(p2 = 0.11142)
ω0 = 0.01238
ω1 = 0.16599
ω2 = 0.59723 | p0 = 0.65160
p = 0.31952
q = 1.61894
(p1 = 0.34840)
ω = 0.15917 |

avrPphD | 6 | 0.3591 | 1.69737 | 1.29E-18 | 2.5E-02 | 5.96E-01 | NP | NP | M3 | −5494.22 | p0 = 0.30676
p1 = 0.3637
(p2 = 0.32954)
ω0 = 0.05915
ω1 = 0.05915
ω2 = 0.96926 | p0 = 0.67219
p = 6.42498
q = 99.00000
(p1 = 0.32781)
ω = 0.97081 |

avrPphE | 15 | 0.2248 | 3.60038 | 3.02E-11 | 3.8E-20 | 7.37E-01 | NP | NP | M3 | −3453.96 | p0 = 0.31937
p1 = 0.59722
(p2 = 0.08341)
ω0 = 0.00001
ω1 = 0.23083
ω2 = 1.04236 | p0 = 0.44450
p = 0.01294
q = 0.03997
(p1 = 0.55550)
ω = 0.21628 |

avrPpiA | 4 | 0.342 | 3.12641 | 5.04E-11 | 8.0E-01 | 9.08E-01 | NP | NP | M3 | −1590.64 | p0 = 0.28033
p1 = 0.28447
(p2 = 0.43521)
ω0 = 0.00993
ω1 = 0.00993
ω2 = 0.77284 | p0 = 0.56549
p = 1.07220
q = 99.00000
(p1 = 0.43451)
ω = 0.77351 |

avrPpiG | 6 | 0.0311 | 75.40503 | 2.48E-58 | NA | 9.9E-01 | NP | NP | M3 | −7405.67 | p0 = 0.21592
p1 = 0.40989
(p2 = 0.37419)
ω0 = 0.00259
ω1 = 0.01926
ω2 = 0.06065 | p0 = 0.98934
p = 0.93298
q = 27.26896
(p1 = 0.01066)
ω = 6.22186 |

holPtoN | 3 | 0.6109 | 50.62056 | 1.22E-76 | 8.3E-84 | 4.1E-78 | 4.50 | 3.50 | M8 | −2347.01 | p0 = 0.34136
p1 = 0.6133
(p2 = 0.04534)
ω0 = 0.01089
ω1 = 0.29653
ω2 = 8.20972 | p0 = 0.96412
p = 0.42451
q = 1.41097
(p1 = 0.03588)
ω = 8.84753 |

holPtoQ | 4 | 0.2741 | 25.89776 | 1.38E-36 | 1.2E-50 | 0.07414972 | 11.10 | 9.30 | M3 | −4716.92 | p0 = 0.42576
p1 = 0.46246
(p2 = 0.11178)
ω0 = 0.00539
ω1 = 0.05947
ω2 = 2.18535 | p0 = 0.90709
p = 0.67503
q = 13.51907
(p1 = 0.09291)
ω = 8.43318 |

holPtoW | 3 | 0.1343 | 10.5815 | 1.85E-21 | NA | NA | NP | NP | M3 | −4886.02 | p0 = 0.30963
p1 = 0.61712
(p2 = 0.07325)
ω0 = 0.00308
ω1 = 0.10674
ω2 = 0.92158 | p0 = 0.40787
p = 0.05149
q = 0.22848
(p1 = 0.59213)
ω = 0.09956 |

hopPmaB | 4 | 0.4784 | 10.95719 | 3.13E-14 | 9.3E-02 | 4.1E-01 | 8 | 3.50 | M3 | −3354.29 | p0 = 0.39762
p1 = 0.5168
(p2 = 0.08558)
ω0 = 0.00001
ω1 = 0.56004
ω2 = 2.20767 | p0 = 0.96484
p = 0.24336
q = 0.38236
(p1 = 0.03516)
ω = 3.04737 |

hopPmaG | 6 | 0.1338 | 8.21425 | 2.21E-45 | 7.3E-73 | 1.1E-01 | NP | NP | M3 | −5526.22 | p0 = 0.2444
p1 = 0.34908
(p2 = 0.40652)
ω0 = 0.00001
ω1 = 0.06712
ω2 = 0.2715 | p0 = 0.74314
p = 0.42775
q = 3.85984
(p1 = 0.25686)
ω = 0.24394 |

hopPmaI | 3 | 0.4228 | 2.3327 | 9.07E-12 | 8.5E-04 | 7.4E-01 | 8.50 | 5 | M3 | −3704.37 | p0 = 0.35997
p1 = 0.55466
(p2 = 0.08537)
ω0 = 0.00001
ω1 = 0.41804
ω2 = 2.23638 | p0 = 0.94869
p = 0.40628
q = 0.92608
(p1 = 0.05131)
ω = 2.51152 |

hopPmaJ | 3 | 0.1659 | 0.80391 | 0.99903 | 1.6E-03 | 9.7E-01 | NP | NP | M3 | −1002.55 | p0 = 0.0513
p1 = 0.93801
(p2 = 0.01069)
ω0 = 0.15336
ω1 = 0.15336
ω2 = 1.3276 | p0 = 0.01487
p = 2.54205
q = 0.00100
(p1 = 0.98513)
ω = 0.15215 |

hopPmaL | 8 | 0.9709 | 3.62074 | 3.55E-17 | 4.0E-04 | 1.8E-03 | 6.80 | 8.20 | M3 | −6003.88 | p0 = 0.39724
p1 = 0.54094
(p2 = 0.06182)
ω0 = 0.13304
ω1 = 0.91632
ω2 = 6.83261 | p0 = 0.93207
p = 0.45587
q = 0.34351
(p1 = 0.06793)
ω = 6.26811 |

hopPtoA | 4 | 0.1998 | 2.60053 | 8.39E-18 | 7.0E-22 | NA | NP | NP | M3 | −4736.63 | p0 = 0.71581
p1 = 0.00000
(p2 = 0.28419)
ω0 = 0.05406
ω1 = 0.35487
ω2 = 0.56702 | p0 = 1.00000
p = 0.37860
q = 1.50673
(p1 = 0.00000)
ω = 0.35156 |

hrpW | 5 | 0.2873 | 16.52812 | 1.46E-37 | 1.7E-39 | 5.6E-02 | 12.50 | 1.50 | M3 | −5321.77 | p0 = 0.28823
p1 = 0.58613
(p2 = 0.12565)
ω0 = 0.00489
ω1 = 0.186
ω2 = 1.4079 | p0 = 0.98450
p = 0.43715
q = 1.53500
(p1 = 0.01550)
ω = 9.53042 |

hrpZ | 11 | 0.2105 | 2.87881 | 6.9E-09 | 1.1E-19 | 4.2E-01 | NP | NP | M3 | −3538.67 | p0 = 0.49306
p1 = 0.20477
(p2 = 0.30217)
ω0 = 0.06795
ω1 = 0.06796
ω2 = 0.53965 | p0 = 0.30370
p = 99.00000
q = 84.99636
(p1 = 0.69630)
ω = 0.06776 |

NP, no positive selection could be detected using this test; NA, the

*P*-value could not be calculated.