Alpha diversity metrics

**Diversity metrics**

**Evenness metrics**

**Other**

**See also **Alpha
diversity

alpha_div_rare command

beta_div command

While many of these alpha diversity metrics are commonly used in OTU analysis, in fact many of them are invalid or hard to interpret for OTUs constructed from NGS amplicon reads.

Name |
Units |
Description |

richness | OTUs |
Number of OTUs with at least one read for the sample. |

chao1 | OTUs |
Chao-1 estimator, calculated as N + S^{2}
/ (2 D^{2}) where N is the number of OTUs, S is the number of singleton
OTUs and D is the number of doublet OTUs, i.e. OTUs with abundance 2. |

shannon_2 | bits |
Shannon
index (logs to base 2). |

shannon_e | nats |
Shannon
index (logs to base e). |

shannon_10 | dits |
Shannon
index (logs to base 10). |

jost | OTUs |
Jost index of order q where q is specified by the
-jostq command-line option, default 1.5. |

jost1 | OTUs |
Jost index of order 1, the
effective number of species given by the
Shannon index. |

Name |
Units |
Description |

simpson | Probability |
Simpson index, calculated as the sum over OTUs of f where
^{2}f is the frequency of the OTU. It is the probability that two randomly
selected reads will belong to the same OTU. A value close to 1 indicates that a
single large OTU dominates the sample, small values indicate that the reads are
distributed over many OTUs. |

dominance |
Probability |
Probability that two
randomly selected reads will belong to different OTUs.
Calculated as 1 – simpson. |

equitability | ? |
Entropy (Shannon index) divided by the logarithm of the number of OTUs. Value of
1 indicates perfectly even (equal abundances), small values indicate a highly
skewed abundance distribution. |

robbins | Frequency |
Robbins index, calculated as S / (N + 1) where S is the number of singleton OTUs
and N is the total number of OTUs. |

berger_parker | Frequency |
Berger-Parker index.
Frequency of the most abundant OTU. A value close to 1 indicates that a single
large OTU dominates the sample, small values indicate that the reads are
distributed over many OTUs. |

Name |
Units |
Description |

reads | Reads |
Total number of reads for the sample. |