Hello, I've recently been studying Ancestral Sequence Reconstruction (ASR), attempting to infer ancestral sequences of viruses. I understand that this inference is constrained by factors like sample size and models, and represents a plausible sequence that may have existed. However, I'm curious about whether directly comparing these inferred ancestral sequences holds biological significance. Can they reflect the differences among the extant sequences from various lineages that were used to infer them?
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Hongzhuang Chen I am afraid that you can lose a lot of information from such comparison. But, it can be applied (and very useful) to illustrate the differences supported statistically by analysis of the original data (sequences).
Thank you, Professor. I truly appreciate your response and the valuable insights you've shared. Alex Ignatov
Homoplasy will likely make inferring the ancestral sequence difficult because repeat mutation at the same positions blurs the lineages.
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