i tried to build a tree between bayesian inference and maximum likelihood algorithm using the same sequence but i got the different result. i reconstructed 5 homolog sequences with no polymorphic site. in maximum likelihood there is no branch length among 5 samples, while in bayesian inference i have branch length among 5 homolog sequence samples. why does this happen ? thank you
I think from its definition, maximum likelihood estimate will be unique but Bayesian estimate will depend on the prior distribution used and that may not be unique. This makes Bayesian estimate not necessarily unique. That accounts for the 5 branches with Bayesian estimation whereas no branch with maximum likelihood estimation.
You really can't "average" Bayesian and Classical ideas. You pay your money and you make your choice, as they say. David Booth
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