One long branch



No model violation
^{1}

Model violation
^{1}


First^{2}

Wrong

Burd SD

Mean SD

Burd ED

Mean ED

First

Wrong

Burd SD

Mean SD

Burd ED

Mean ED

ML^{3}

30

56

144

2.57

56

1.00

20

65

164

2.52

65

1.00

BUU

30

46

232

5.04

46

1.00

20

50

222

4.44

50

1.00

BGU

30

36

96

2.67

36

1.00

20

39

118

3.03

39

1.00

BGE

30

28

88

3.14

28

1.00

20

39

116

2.97

39

1.00

Two long branches


No model violation

Model violation


First

Wrong

Burd SD

Mean SD

Burd ED

Mean ED

First

Wrong

Burd SD

Mean SD

Burd ED

Mean ED

ML

20

186

1124

6.04

273

1.47

20

174

1166

6.70

207

1.19

BUU

20

237

1854

7.82

326

1.38

10

244

1900

7.79

299

1.23

BGU

20

87

270

3.10

104

1.20

20

105

468

4.46

119

1.13

BGE

20

86

314

3.65

101

1.17

20

115

650

5.65

131

1.14

 ^{1} Proteinsequence data were evolved under the Jones et al. (JTT) or, alternatively, mammalian mitochondrial (mtmam) model of sequence change, and trees were inferred assuming the JTT model.
 ^{2} Performance was measured by six indices: First, the lowest investigated branchlength ratio at which at least one inaccurately reconstructed tree was found; Wrong, the number of inaccurately inferred trees out 400 (8 branchlength ratios × 50 replicates at each ratio); BurdSD, the bipartition burden, calculated as the RobinsonFoulds symmetric distance by which each tree differs from the known tree, summed over the 400 trees; MeanSD, the mean RobinsonFoulds symmetric distance per inaccurate tree; BurdED, the edit burden, calculated as the edit distance by which each tree differs from the known tree, summed over the 400 trees; and MeanED, the mean edit distance per inaccurate tree.
 ^{3} Inference methods: ML, protein maximum likelihood with gamma ASRV correction; BUU, Bayesian inference, uncorrected for ASRV, uniform prior; BGU, Bayesian inference, gamma ASRV correction, uniform prior; and BGE, Bayesian inference, gamma ASRV correction, exponential prior. See text for further details.