Cause of huge number of low-probability nodes about linearham HOT 6 CLOSED

My guess (without knowing anything about the family) is that the ASR is more uncertain due to the data loss and is just confused about substitution order. Looking at the image, I do see a somewhat certain path, does that path exist in the larger family graph too?

from linearham.

hmm, that sounds promising. @mmshipley does it seem possible that the main results are pretty much the same, there's just more low probability cruft? Maybe we can solve this as more a visualization problem, maybe don't display nodes below a certain probability (well i'm assuming that's what the filtering settings do, in which case I guess I'm suggesting maybe we can make the filtering settings smarter?).

from linearham.

She says yes, it seems likely that the main results end up the same. But I think it's still a real problem if it's easy to get diagrams like that ^ out, since most people will probably have the same response and ignore it and/or assume something's wrong (as happened here) so probably worth working on the filtering settings.

from linearham.

Yes, that makes sense, the filtering settings aren't perfect. FYI, I basically filter on edge probabilities (i.e. keep all edges if prob >= CUTOFF), maybe adding some node logic might improve it

from linearham.

Great. And thanks again for responding promptly, this is really helpful. It looks like jared will work on this in a month or so.

from linearham.

It seems like a better title for this at this point would be "fiddle with threshold settings for lineage path plotting", which is maybe worth doing, but without a working example that does something we don't like, I don't think there's any point in keeping this issue open.

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