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Phylotype analysis

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Revision as of 19:17, 16 May 2012 by Mbakker (Talk | contribs) (Added description for phylo.diversity)

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General commands

  • Classify.seqs - Classify sequences according to a taxonomy corresponding to a reference taxonomy
  • Phylotype - assign sequences to OTUs based on their taxonomy
  • phylo.diversity - calculate diversity based on cladistic relationships among a set of taxa
  • classify.otu - find a consensus taxonomy for an OTU
  • classify.tree - find a consensus taxonomy for each node on a tree
  • get.lineage - selects sequences from a given taxonomy
  • remove.lineage - removes sequences from a given taxonomy
  • summary.tax - summarizes taxonomy data