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Table 4 Topological accuracy of single-gene phylogenies

From: Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

VERTEBRATA

version

mean

loss (%)

RAW

65.64%

NA

RAW (long)

68.85%

NA

HMM

65.23%

5.61

HMM-L

65.41%

4.22

HMM-LS

65.58%

2.68

PREQUAL

65.73%

3.06

BMGE

64.83%

4.83

TrimAl

65.28%

1.8

HMM Random

64.56%

5.61

HMM + BMGE

63.94%

13.38

HMM + TrimAl

62.90%

13.76

MIN

68.71%

0.71

MIN + HMM

68.67%

6.43

MAMMALIA

version

mean

loss (%)

RAW (NT)

63.19%

NA

RAW (NT long)

69.77%

NA

HMM (NT)

66.29%

2.92

HMM-L (NT)

66.13%

2.57

HMM-LS (NT)

65.75%

2.12

PREQUAL (NT)

64.77%

2.92

BMGE (NT)

63.59%

3.16

TrimAl (NT)

63.77%

3.76

HMM Random (NT)

62.59%

2.92

HMM + BMGE (NT)

66.56%

4.7

HMM + TrimAl (NT)

66.45%

5.16

RAW (AA)

45.29%

NA

RAW (AA long)

53.59%

NA

HMM (AA)

46.98%

2.92

HMM-L (AA)

46.65%

2.57

HMM-LS (AA)

46.48%

2.12

PREQUAL (AA)

45.63%

2.92

BMGE (AA)

45.45%

3.16

TrimAl (AA)

45.36%

3.76

HMM Random (AA)

44.56%

2.92

HMM + BMGE (AA)

46.52%

4.7

HMM + TrimAl (AA)

46.64%

5.16

  1. 1mean: average frequency of correctly recovered clades, 2loss: fraction of residues removed from the raw MSAs. 3long: Values for the half longest MSAs. See the legend of Fig. 6 for the complete set of abbreviations