Nucleotide Sequence Optimization

NUPACK - analysis and design of nucleic acid structures, devices, and systems.

http://nupack.org/

DNA Chisel - a versatile sequence optimizer

paper on bioinformatics

https://academic.oup.com/bioinformatics/article/36/16/4508/5869515

doc website

https://edinburgh-genome-foundry.github.io/DnaChisel/index.html

online demo

https://cuba.genomefoundry.org/sculpt_a_sequence

optipyzer

Multi-Species Codon Optimization Engine

https://github.com/NLeRoy917/optipyzer

CONTRAfold

http://contra.stanford.edu/contrafold/download.html

Codon Harmony

https://codon-harmony.readthedocs.io/en/latest/readme.html#features