Zamin Iqbal
Zamin Iqbal
These must always be horizontally offset, right? Is it possible for this to happen with just one leve of nesting? I guess the answer is yes, you can delete an...
is it possible without indels? i guess not?
Doh, of course
Rachel says couyld you please put the MSAs that generated these examples in?
I will propose that the only thing you need to avoid is having two different source/sink paths which spell the same sequence.
i think it's an interaction of - the MSA (can we rely on the MSA algorithm to align the same sequence the same way on two different lines?) - the...
i actually think you might fix it by using smaller kmers in the clustering
yes, all changes may cause bugs. but smaller kmers for clustering would detect small repeats.
but i think we need a list of 5 or 10 examples of where it happens, with their MSAs
We need examples before we speculate - intuition from data and then move to possible solutions. one issue is that we drop a vertical slice down a matching kmer, marked...