Zulko

Hello! The short answer is that DNA Chisel was not originally developed with solution diversity in mind, but there are workarounds to achieve this. Off the top of my head:...

I am not against it but I tried it at some point but met issues, I don't remember the details but that created a weird circular import problem in the...

That's a complex problem, and I don't think it can be done efficiently by changing how ``optimize`` works. A lot of the optimization efficiency comes from the way the specifications...

Let's keep this open as an un-resolved issue at the moment for other people to find.

Sorry I didn't get what `use_breach_form` means, could you give an example of the ideal code you'd write and what it would do?

ViennaRNA or any other package would be a priori as easily integratable with DNAChisel as with D-tailor. There is no example yet in DNA Chisel because I am not sure...

It's true that more specialized software may mutate the sequence in a more rational, structure-oriented way than Chisel does. One way to improve Chisel's performance would be to return well-target...

Good points thanks for the report. When you use a TaxID, Chisel will use the [codon-usage-tables](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables) library to get that dictionnary, so I guess the fix should happen at the...

> @Zulko do the frequencies need to add up exactly to 1? For example the stop codon in the link adds up to 0.30 + 0.24 + 0.47 = 1.01...

My two cents on this is that this would be a great constraint to support since Twist is enforcing it, but it might also be a tricky to resolve, in...