Removed unnecessary print statement.
Changed default selections of what is printed to the log file. It is now
just the alignment, log likelihood, and acceptance rates. The trees are
just outputted to the .tree and .ctree files by default. 

Also now the MPD alignment plugin outputs the marginal probabilities to
a separate file, to make it easier for people to read in the alignment
without having to remove the scores from the end of the file.