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OTU-based approaches

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OTU-based approaches enable you to analyze the frequency distribution of sequences found in bins using a variety of methods. In contrast to hypothesis testing approaches, these methods allow you to quantify ecological features such as richness, diversity, and similarity. Prior to running any of the below listed commands, you will need to do some sequence processing. Examples of each command are provided within their specific pages, but several users have provided several analysis examples, which use these commands. An exhaustive list of the commands found in mothur is available within the commands category index. Also list of mothur's calculators with detailed examples.


General commands

  • dist.seqs - generate a column or phylip-formatted distance matrix
  • cluster - clustering sequences into OTUs based on genetic distance
  • hcluster - clustering sequences into OTUs based on genetic distance
  • cluster.classic - clustering sequences into OTUs based on genetic distance
  • get.rabund - convert list or species-abundance data into rank-abundance data
  • get.sabund - convert list or rank-abundance data into species-abundance data
  • bin.seqs - identify the OTU that each sequence belongs to
  • get.oturep - identify a representative sequence from each OTU
  • get.group - have mothur remind you what group identifiers are found in your shared files
  • get.label - determine the OTU definitions that are found in your OTU files
  • get.otulist (was get.listcount) - list sequences by OTU number
  • make.group - generate a group file
  • make.shared - create a shared file from a list and group file
  • otu.hierarchy - relates OTUs at different distances
  • parse.list - parses a list file by group
  • classify.otu - find a consensus taxonomy for an OTU
  • split.abund -
  • normalize.shared
  • sub.sample
  • remove.groups - remove sequences from a specific group or set of groups from a list file
  • get.groups - select sequences from a specific group or set of groups from a list file
  • get.otus - selects OTUs containing sequences from a specific group or set of groups
  • remove.otus - removes OTUs containing sequences from a specific group or set of groups
  • get.dists - selects distances related to sequences or groups in an accnos file.
  • remove.dists - removes distances related to sequences or groups in an accnos file.
  • consensus.seqs
  • make.biom - creates a .biom file from a shared file.
  • primer.design - - will generate candidate PCR primers for OTUs of interest

Single sample analyses

Multiple sample analyses