The Library

This section is for those users comfortable with Python programming.

Contents

• 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
• Usage Examples
  • Data manipulation
    • Translating DNA into protein
    • Advanced sequence handling
    • Complete version of manipulating sequence annotations
    • Getting the reverse complement
    • Map protein alignment gaps to DNA alignment gaps
    • Data Manipulation using Table
    • Manipulation of Tree Node Objects
    • An Example of Conditional Tree Node Modifications
  • General data analysis
    • Estimating periodic signals
  • Modelling Evolution
    • The simplest script
    • Performing a relative rate test
    • A test of the neutral theory
    • Allowing substitution model parameters to differ between branches
    • Using codon models
    • Use an empirical protein substitution model
    • Likelihood analysis of multiple loci
    • Simulate an alignment
    • Performing a parametric bootstrap
    • Perform a coevolutionary analysis on biological sequence alignments
    • Analysis of rate heterogeneity
    • Evaluate process heterogeneity using a Hidden Markov Model
  • Phylogenetic Reconstruction
    • Calculate pairwise distances between sequences
    • Make a neighbor joining tree
    • Make a UPGMA cluster
    • Phylogenetic reconstruction by least squares
    • Making a phylogenetic tree from a protein sequence alignment
• Data Files Used in the Documentation
• API
  • Objects for the major data types
    • alignment
    • sequence
    • table
    • tree