I have X sequences sampled over a Y year time span; are they enough to estimate the substitution rate?
It depends on the substitution rate. If the substitution rate is high enough to produce a substantial number of substitutions in the Y years then it may work. The easiest thing is to simply try it and see. It would be best to start with a simple model – HKY, constant population size and a strict molecular clock. If that seems to behave well then you might consider a more realisitic model, depending on the question you are trying to answer. If the time span is insufficient to provide information about the substitution rate then BEAST will not converge and the age of the root of the tree will simply increase to a very large value (and the rate will drop towards zero).
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