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 …
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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.
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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More seriously, I am concerned that there is an increasing trend to infer phylogenies on highly divergent viruses that share almost no sequence similarity and where the alignment is dubious at best. Beware of crap alignments.
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Totally agree - problem is that no matter the MSA you *always* get an answer - the art is in determining whether you can trust that answer or not. Which, unfortunately, isn't easy. We need a new tool - AlCrap - it'll tell you whether your alignment is crap or not...
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Whatever!
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