Jerome Kelleher

I was thinking of doing it as a for-loop over chromosomes, but maybe this wouldn't work at all actually and we do need to process all edges for a given...

I'm with @bhaller here on the 'not right now, thanks' assessment. The idea came up during a discussion and I wanted to get some feedback on what would be involved...

I think it's a reasonable thing to do. I guess it is technically breaking, but we could roll it in for 0.5.0?

I remember going through this, and it turns out to be quite tricky in the general case of lots of mutations at a site to know that it's fixed. I...

Basically, yeah. But this won't handle funky situations where we have (say) n mutations to 1 over the leaves, will it? But, we should be able to build an allele...

Really? The site is still monomorphic right? What's the difference?

I see that, but it's a statement about the sequences we're making, not the ancestry I would have thought. The semantics will get weird and strained if we don't I...

Ah, I see. Should we add a ``filter_fixed_simple_sites`` (or something) option to simplify then? I think catching the single mutation fixed sites is pretty easy? I don't want to call...

> ps. we should make an "allele frequency" function, which we can do as above. +1

> Just filter_fixed_mutations should do it? (i.e., fixed mutations, not fixed alleles...) ... Yeah, OK. But this implies that we only remove the mutation, not the site. However, if this...