Taking into account alignment uncertainty

WrightFisher talks about a paper & the commentary in Science describing how alignment uncertainty should be taken into account when doing phylogenetic analyses on genomic datastets (some might call this phylogenomics, but Dr Eisen won’t). If the sequence alignment is treated as a random variable (and in bayesian approaches have a prior based on result(s) from an alignment program) then more accurate reconstruction. Robin points out several statistical alignment approaches that do just this including TKF91 and recent work that unifies a probabilistic framework with transducers.

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