Fortunately, there are many phylogeny programs that are. Even more fortunately, there are systematists that can present data for which computer analysis need not be required. My linked to alignment, for example.
I guess a 40 million year split wasn't quite good enough...
Basically, the 'letters' you can see represent the nucleotides in the sequence that differ from the top sequence (reference sequence). At 21 sites in, you can see a number of species have an 'A', for example. All of them happen to be Old World monkeys. Such patterns can be found throughout the alignment.
The abstracts linked to by Dr.Caporale deal with the potential difficutlis in phylogenetic analyses due to non-random mutations and other occurrances that can obscure 'true' phylogentic reconstruction. The abstracts, however, iindicate that while there are potential problems, sufficiently large datasets and programs that take such possibilities into account can compensate.
That is, it "non-random mutation" is only aproblem for phylogeny if one does not take it into account. Unfortunately for Borger, who claims that NRM essentially falsify all phylogenetic reconstructions, it is at best a minor problem.