**API-breaking changes:**
- The strand on which to look for a pattern in AvoidPattern and
EnforcePatternOccurence is not given by the location (strand 1, -1, or strand
0 to look in both strands).
- AvoidNonUniqueSegments renamed in UniquifyKmers
- Complete rewrite of CodonOptimization, method names are now use_best_codon,
**New features**
- Support for different genetic codes in EnforceTranslation.
- Support for non-standard start codons in EnforceTranslation
- New AvoidMatches specification based on Bowtie.
- AvoidChanges and EnforceChanges can now tunable (EnforceChanges(60%),
AvoidChanges(max_edits=2))
- New SequencePattern MotifPssmPattern.
**Misc.**
- Got rid of some tables like Genetic code, now taken from Biopython.
- Complete code restructuring by cutting large files into smaller ones.