See the debate on how to infer RNA virus origins from phylogenies: https://mbio.asm.org/content/10/2/e00289-19 … and the response. Interested parties should definitely check out the original alignments (especially Data Set S2) herehttps://mbio.asm.org/content/9/6/e02329-18 …
The response by the authors.... so weird. Totally agree with you - that MSA is completely meaningless!
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I thought these Letters were limited to 500 words?! I particularly liked the line about the median distance between the RTs and RdRps being 5 amino acid substitutions per site. Phew - that's alright then.
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That's the funny thing - they started with laying out pretty well why it can't be done. Then went on to saying, "but we did it anyway". And then finished with, "but yeah, probably can't be done, but hey, whatever!"
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