I am writing to ask how WAAFLE infers the direction of HGT events. WAAFLE assigns directionality to syntenies such as ABA, AB~A, and ABA~A, but not to patterns such as ABABA, ABA*A, AB*AA, ABA~*A, or AB~*AA.
Could you clarify the rationale for this? I would have expected some of these patterns to be directional if direction is considered at the level of individual genes rather than the entire contig. For example:
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ABABA could be interpreted as containing two B>A transfer events.
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Because
*denotes a gene assigned to both taxa, I would not consider it a transferred gene itself. I would therefore expect it not to affect the inferred direction of the adjacent B gene in patterns such as ABA*A, AB*AA, ABA~*A, or AB~*AA. This seems analogous to ignoring genes marked with~.
For example:
| Synteny | Default direction | Possible interpretation | Proposed direction |
|---|---|---|---|
| ABABAA | A?B | ABABAA ā ABA + ABAA | B>A, B>A |
| ABAAA* | A?B | Ignore *, or assign * to A |
B>A |
| AB*AAA | A?B | Ignore *, or assign * to A |
B>A |
| AB~A | B>A | ABA after ignoring ~ |
B>A |
I would be very interested to know whether this behaviour reflects a deliberate conservative rule in WAAFLE, and if so, what motivated that choice.
Thank you for your time and efforts.