DReichLab / DReichLab/AdmixTools
Using f3 to test gene flow from ghost species
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- Dominant language
- C
- Stars
- 235
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
Description
I ask you this question to check if my logic makes sense.
Suppose this phylogeny (A, (B,C)), and we want to test gene flow from ghost species outside of this tree to C. In this case, we expect the overrepresentation of this genotype: 0, 0, 1 for A, B, and C, respectively. Then, f3 = (c-a)(c-b)=(1-0)(1-0) = 1 > 0.
Thus, if f3 > 0, it supports the existence of gene flow from ghost species.
Does it makes sense?
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
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Research direction
The issue discusses f3, the topology (A, (B,C)), and a proposed genotype pattern, but names no source file, test, or entry point. Start by checking the f3 definition and whether the stated interpretation follows from the described topology; done would be a maintainer-confirmed explanation or correction.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100