PyCogent 1.9 documentation
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Manipulating biological data¶

Sequences¶

  • Loading nucleotide, protein sequences
  • Using the MolType and Sequence objects
  • Alphabets
  • DNA and RNA sequences
  • Protein sequences
  • Collections and Alignments
  • Annotations
  • Annotations with coordinates

Genetic code¶

  • Getting a genetic code
  • Translate DNA sequences
  • Translate all six frames
  • Find out how many stops in a frame
  • Translate a codon
  • Look up the amino acid corresponding to a single codon
  • Or get all the codons for one amino acid
  • For a group of amino acids
  • Converting the CodonAlphabet to codon series
  • Obtaining the codons from a DnaSequence object

Trees¶

  • Trees
  • Phylonodes Methods

Tables¶

  • Tabular data

Structures¶

  • Structural data
  • Structural Data Advanced
  • Intramolecular contacts

PyCogent News and Announcements

Table Of Contents

  • Quick installation using pip
  • The Readme
  • Coding guidelines
  • The data files used in the documentation
  • Cogent Usage Examples
  • PyCogent Cookbook
  • For Developers
  • Scripting guidelines
  • Licenses and disclaimer
  • Changelog

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