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OTU-based approaches

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Revision as of 18:18, 17 November 2009 by Westcott (Talk | contribs) (General commands)

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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.

General commands

  • dist.seqs - generate a column or phylip-formatted distance matrix
  • read.dist - read in distance matrices for downstream analysis
  • cluster - clustering sequences into OTUs based on genetic distance
  • hcluster - clustering sequences into OTUs based on genetic distance
  • read.otu - read OTU profiles into mothur
  • 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.line - determine the line number in a file for each OTU label
  • get.listcount - list sequences by OTU number

Single sample analyses

Multiple sample analyses

  • collect.shared - generate collectors curves using a variety of β-diversity calculators
  • rarefaction.shared - generate an inter-sample rarefaction curve for the observed number of OTUs
  • summary.shared - calculate a variety of β-diversity calculators for each OTU definition
  • dist.shared - generate a phylip-formatted distance matrix describing the pairwise similarity between samples using various calculators
  • get.sharedotu - identifies sequences that are shared by multiple OTUs
  • heatmap.bin - generate an svg-formatted heatmap for your OTU data
  • heatmap.sim - generate an svg-formatted heatmap describing the similarity between samples using various calculators
  • venn - generate 2, 3, or 4-way venn diagrams to describe the overlap between samples using various calculators
  • tree.shared - generate a newick-formatted dendrogram comparing communities using various calculators