Marcel

Awesome! > I still could not figure out how to construct a partial order graph using in seqan2. I did try to visualise the alignment graph constructed by seqan. It...

Hi @tloka, thank you for the input :) One of our initial design goals for alphabets were to disallow initialising an alphabet by builtin types. For some reasons we did...

> For your last suggestion, wouldn't something like this > > ```c++ > auto cutoff_phred = 14_phred42; // short for seqan3::phred42.assign_phred(14) > ``` > > again produce the same ambiguity...

I have just glanced through all comments, and I'm not sure if you already suggested this. Maybe we should add a notice box to all member functions that are there...

Hi Robin, thank you for your excellent and helpful write-up of your use case. I'm unfortunately not too familiar with MSA and my answer might lack understanding. Furthermore, two of...

Sorry for the late response, I'm terrible at keeping conversations alive 🙈 I sketched for (1) a solution in seqan3, the basic idea is to align the subsequences without the...

> Is it possible to force the final character of my chosen string to align as a match somewhere in the graph? For (2) I think this is not possible...

No, this should definitely work! The second example is a semi-global alignment with the twist that an "T" end char in the first sequence has zero cost to any other...

Yeah, this is not implemented, yet. But, I think as this functionality is "just" ™️ a swap of the gap extension definition within the recursion formula, this should be definitely...

We merged the patch, but we still want to evaluate if the patch is the version we want.