Model condition | Number of taxa | Tree height | Insertion/deletion probability | NHD | Gappiness | True align length |
---|

10.A | 10 | 0.4 | 0.13 | 0.297 | 0.474 | 1965.3 |

10.B | 10 | 0.7 | 0.1 | 0.394 | 0.512 | 2165.1 |

10.C | 10 | 1 | 0.06 | 0.514 | 0.526 | 2162.8 |

10.D | 10 | 1.6 | 0.031 | 0.599 | 0.485 | 1874.4 |

10.E | 10 | 4.3 | 0.013 | 0.693 | 0.465 | 1849.3 |

50.A | 50 | 0.45 | 0.06 | 0.281 | 0.516 | 2043.5 |

50.B | 50 | 0.7 | 0.03 | 0.398 | 0.475 | 1935.5 |

50.C | 50 | 1 | 0.02 | 0.514 | 0.498 | 2047.6 |

50.D | 50 | 1.8 | 0.012 | 0.594 | 0.471 | 1945.0 |

50.E | 50 | 4.3 | 0.004 | 0.688 | 0.459 | 1890.2 |

- The main simulations in our study utilized the medium gap length distribution from the study of Liu et al. [15]. The model condition parameters consist of the number of taxa, model tree height, and insertion/deletion probability. Each model condition corresponds to a distinct set of model parameter values. The 10-taxon model conditions are named 10.A through 10.E in order of generally increasing sequence divergence; the 50-taxon model conditions are named 50.A through 50.E similarly. The following table columns list average summary statistics for each model condition (\(n=20\)). “NHD” is the average normalized Hamming distance of a pair of aligned sequences in the true alignment. “Gappiness” is the percentage of true alignment cells which consists of indels. “True align length” is the length of the true alignment