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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