Input: Sequence Set , Minimum Length with Polymers *l, *Neighborhood |

Parameter , Clustering Threshold , MinClusterSize |

* *Output: Clustering Result of Sequence Set |

{ |

Seed = ; // Initialize the Seed Sequence Set |

For ++ // Traverse the Distance of the Input sequence and current Seed Set |

* * For ++ // Compute Distance of and (or Simmilary); |

If Meet Distance , |

// then Sequence Clustering Unit of , and output |

* *, ; |

Else |

// with Neighbor Sequence Expanding Method, yield to Neighbor Sequence () |

, // Expanding Current Seed Sequence Set |

; |

End If |

* *End For |

END For // Travel all of Clustering Units, Subtract the Clustering Results the Parameter |

MinClusterSize |

, |

Reassigned () // Recluster Sequence in Clustering Units base on the Nearest |

Neighbor Clustering Algorithm, Assigned to the nearest cluster units , and Meet |

End If |

} |

Notes: denotes the th Seed Sequence in Sequence Set; Neighbor () denotes |

Neighbor Sequence (); denotes Clustering Unit of . |