Significance measure | Spearman’s correlation with true \(t_{\text {MRS}}\) |
---|

\(t_{\text {MRS}}(q<0.01)\) | 0.965 |

\(t_{\text {MRS}}(q<0.1)\) | 0.938 |

\(t_{\text {MRS}}(q<1)\) | 0.858 |

Reconstruction (\(q<1\)) | 0.905 |

Alignment (\(q<1\)) | 0.338 |

Entropy | 0.301 |

Pairwise | 0.344 |

Phastcons | 0.112 |

Phylop | 0.108 |

Gerp | 0.129 |

- We show Spearman’s correlation coefficient with the true \(t_{\text {MRS}}\) obtained from simulation and several measures for nucleotide conservation. The first three columns represent \(t_{\text {MRS}}\) computed by our exact algorithm with filtering by
*q* values. ‘reconstruction’ represents approximate \(t_{\text {MRS}}\) values estimated from reconstruction of ancestral states. ‘alignment’ represents approximate \(t_{\text {MRS}}\) values estimated from closest extant species which has different nucleotide base from the nucleotide of the target species. ‘entropy’ represents the negative information entropy of the base frequency of alignment column. ‘pairwise’ represents the pairwise alignment similarity of alignment column. ‘phastcons’ represents the posterior probability of conservation at the alignment column. ’phylop’ represents the p-values of negative selection. ‘gerp’ represents the ‘rejected substitution’ values