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  HyPhy Documentation: Result Processing: Reconstruct Ancestral Sequences

      Summary:  Ancestral Sequences is a result processing tool which allows the user to reconstruct the ancestral sequences using the most recent MLE and save them to a file.

   The ancestral sequences are reconstructed by assigning characters to internal tree nodes so that the likelihood of the tree(s) with those assignments is maximized over all possible internal node states (given current parameter estimates).
   When rate variation is present, the following method is used (suggested by Jesse Taylor): for each site, we compute the posterior distribution of rate class assignments using current parameter estimates. Next, for each site, we choose the rate with highest posterior probability, and reconstruct ancestral states for that site using that rate.

     Options: If more than one likelihood function is available, a prompt will appear, listing all the likelihood functions.
    The user will also be asked what file the results should be saved to. The format of the data file is determined by the default setting which can be modified via the preferences box.

     Output:  Reconstructed ancestral sequences saved to a file.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002