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Table 1 Sensitivity and specificity of HmmCleaner

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

matrix name c1 c2 c3 c4 global sensitivity global specificity sensitivity for 50 seqs specificity for 50 seqs
default −0.150 −0.080 0.150 0.450 94.26% 94.42% 98.42% 93.97%
species-rich −0.175 − 0.175 0.150 0.400 85.70% 97.02% 97.36% 96.48%
high-specificity −0.125 −0.125 0.175 0.400 88.89% 97.34% 96.64% 97.08%
species-rich and high- specificity −0.125 − 0.125 0.150 0.400 74.03% 98.78% 94.11% 98.56%
HmmCleaner 1.8 −0.300 −0.100 0.200 0.500 94.56% 91.57% 98.74% 90.73%
  1. The four new scoring matrices provided with HmmCleaner v2 and the scoring matrix equivalent to HmmCleaner v1.8 for comparison. c1-c4: values of the elemental scores for the four levels of residue conservation provided by HMMER. Global sensitivity and specificity were computed across all conditions of simulation, whereas the last two columns only used the most species-rich MSAs