For example, the " ape " package in the statistical computing environment R also provides methods for ancestral state reconstruction for both discrete and continuous characters through the " ace " function, including maximum likelihood . ( Note that " ace " performs reconstruction by computing scaled conditional likelihoods instead of the marginal or joint likelihoods used by other maximum likelihood-based methods for ancestral reconstruction, which may adversely affect the accuracy of reconstruction at nodes other than the root . ) Phyrex implements a maximum parsimony-based algorithm to reconstruct ancestral gene expression profiles, in addition to a maximum likelihood method for reconstructing ancestral genetic sequences ( by wrapping around the baseml function in PAML ).
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