User GuideΒΆ This guide introduces the main concepts in Codeine, via various worked examples. Contents: Coding spaces Counting Sampling Enumeration Validation Translation tables Choosing a translation table Custom tables RNA tables Available tables Fixed codons Sequence contexts Adding constraints Forbidden motifs Max homopolymer Tandem repeats Combining constraints Empty spaces Codon weights Species-specific weights Custom weights Zero weights Weight thresholds Mutation spaces Creating a mutation space Distance constraints Constraining free positions Enumerating & sampling variants Inherited constraints