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.
|