cogent3

Navigation

  • Warning
  • Installation
  • The apps
  • Visualisation Capabilities
  • The Library
    • Cookbook
    • Usage Examples
    • Data Files Used in the Documentation
    • API
  • License

Related Topics

  • Documentation overview
    • The Library
      • Cookbook
        • Previous: Cookbook
        • Next: Molecular types

Quick search

Manipulating biological data¶

Sequences and Alignments¶

  • Molecular types
  • Loading nucleotide, protein sequences
  • Alphabets
  • Sequence
  • Protein sequences
  • Collections and Alignments
  • Annotations
  • Annotations with coordinates

Genetic code¶

  • Available genetic codes
  • Getting a genetic code with get_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
©2020, cogent3. | Powered by Sphinx 1.8.5 & Alabaster 0.7.8 | Page source