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petrelharp / ftprime_ms

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Added asy source for rough version of diagram. #9

Closed jeromekelleher closed 6 years ago

jeromekelleher commented 6 years ago

Rough outline of the figure with sites and mutations. I have a few ideas for making it better:

  1. Add a time scale for the trees
  2. Add mutational states for all the samples on the bottom (underneath ID label)
  3. Possibly add state transitions to the mutation labels (i.e. C->G)
  4. Maybe reclaim some x-space by mutations table underneath the sites table. (Not certain this will look good though, and might end up confusing).

Also short discussion of sites and mutations.

petrelharp commented 6 years ago

Looks good. If the diagram contains all the information in the tables, that'd make it a very useful illustration. I'm in favor of all proposed ideas 1--4.

jeromekelleher commented 6 years ago

Cool. I'll update the diagram and make a pass at the rest of the text for this section tomorrow.

jeromekelleher commented 6 years ago

I've added some more discussion here based around an example simulation in msprime. I think this is an OK-ish first pass at this section, so we might as well merge this much. I'll make another pass at the diagram and text after going through some other stuff.

Any thoughts @petrelharp?

petrelharp commented 6 years ago

great. merging.