Calculators

The following are a list of calculators currently available in mothur for OTU-based analyses. If there is a calculator that you think should be added, please consider either contributing your code or asking us to add it to our list of features for future versions of mothur. Following the links will take you to pages describing the formulae and example calculations using the Amazonian dataset.

Community richness

  • sobs - the observed richness
  • chao - the Chao1 estimator
  • ace - the ACE estimator
  • jack - the jackknife estimator
  • bootstrap - the bootstrap estimator

Community evenness

  • simpsoneven - a Simpson index-based measure of evenness
  • shannoneven - a Shannon index-based measure of evenness
  • heip - Heip’s metric of community evenness
  • smithwilson - Smith and Wilson’s metric of community evenness

Community diversity

Estimates of number of additional OTUs observed with extra sampling

  • boneh - Boneh’s estimator
  • efron - Efron’s estimator
  • shen - Shen’s estimator
  • solow - Solow’s estimator

Statistical distributions

  • logseries - tests whether observed data follow the log series distribution
  • geometric - tests whether observed data follow the geometric series distribution
  • bstick - tests whether observed data follow the broken stick distribution

Shared community richness

  • sharedsobs - the observed richness shared between two or more samples
  • sharedchao - the two or more sample shared Chao1 richness estimator
  • sharedace - the two sample shared ACE richness estimator

Similarity in community membership

  • anderberg - the Anderberg similarity coefficient
  • hamming - the Hamming distance
  • jclass - the traditional Jaccard similarity coefficient based on the observed richness
  • jest - the Jaccard similarity coefficient based on the Chao1 estimated richnesses
  • kulczynski - the Kulczynski similarity coefficient
  • kulczynskicody - the Kulczynski-Cody similarity coefficient
  • lennon - the Lennon similarity coefficient
  • memchi2 - the membership-based Chi-squared distance
  • memchord - the membership-based Chord distance
  • memeuclidean - the membership-based Euclidean distance
  • mempearson - a membership-based version of the Pearson correlation coefficient
  • ochiai - the Ochiai similarity coefficient
  • sorclass - the Sorenson similarity coefficient based on the observed richness
  • sorest - the Sorenson similarity coefficient based on the Chao1 estimated richnesses
  • whittaker - the Whittaker similarity coefficient

Similarity in community structure

Utility calculators

  • nseqs - the number of sequences in a sample
  • sharednseqs - the number of sequences in two samples