Open hyanwong opened 2 years ago
Similarly for other mentions of "alleles" in that notebook, I would say, e.g. "Suppose we have a sample of 4 alleles" - I think you mean genomes here. I could see the current phrasing as meaning 4 alleles at a single site.
Thanks @hyanwong! I'm trying to introduce them first to the idea of a tree at a single point in the genome, would 'nucleotide' be a better choice? (Though I know the sites can be other things, I don't want to introduce that level of abstraction just yet) Then after that I basically say "this single tree might also represent the genealogy at some neighbouring sites, but at some point you'll move along the genome and see a different tree, and that's why it is a tree sequence"
On Thu, 9 Jun 2022, 5:16 pm Yan Wong, @.***> wrote:
Similarly for other mentions of "alleles" in that notebook, I would say, e.g. "Suppose we have a sample of 4 alleles" - I think you mean genomes here. I could see the current phrasing as meaning 4 alleles at a single site.
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Hmm, well an allele is something different, right? Two sample nodes can contain the same allele at a locus. The node is not an allele itself.
Could you just say " the nodes represent genomes or regions of genomes, here we've picked a short region and so the relationship is just a simple tree" - or something?
Yes, I guess I could say "a region spanned by a single nucleotide base"
Or "a short region of genome, perhaps just a single base"?
You say
But I think it might be read as the nodes representing alleles (which they don't, of course). We normally say that the nodes represent genomes, I think? The genomes can carry mutations, which result in alleles being observed.