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Cookbook¶

  • Manipulating biological data
    • Sequences and Alignments
    • Genetic code
    • Trees
    • Tables
  • Building alignments
    • Using the cogent3 aligners
    • Converting gaps from aa-seq alignment to nuc seq alignment
  • Genetic distance calculation
    • Fast pairwise distance estimation
    • Computing genetic distances using the Alignment object
    • Using the distance calculator directly
    • Likelihood based pairwise distance estimation
  • Building phylogenies
    • Building A Phylogenetic Tree From Pairwise Distances
    • Directly via alignment.quick_tree()
    • By Least-squares
    • By ML
  • Evolutionary Analysis Using Likelihood
    • Specifying substitution models
    • Making a likelihood function
  • Useful Utilities
    • UnionDict – a dict with set like operations and keys as attributes
    • Using Cogent3’s optimisers for your own functions
    • Miscellaneous functions
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