User Guide

This guide introduces the main concepts in Codeine, via various worked examples.

Contents:

• Basic usage
  • Counting
  • Sampling
  • Enumeration
• Adding constraints
  • Forbidden motifs
  • Max homopolymer
  • Fixed codons
  • Combining constraints
• Sequence contexts
• Mutation spaces
  • Creating a mutation space
  • Distance constraints
  • Constraining free positions
  • Enumerating & sampling variants
  • Inherited constraints
• Translation tables
  • Choosing a translation table
  • Custom tables
  • RNA tables
  • Available tables
• Codon weights
  • Species-specific weights
  • Custom weights
  • Zero weights
  • Weight thresholds