I had originally posted a link to this alignment when Borger asked for some evidence for NDT. One familiar with DNA sequence data will immediately see why that is. It came up again in this thread.
Borgern then thought he had stumbled onto something, and asked about two of the species in the alignment, coded as Tob and Cap. He wondered why there was such a difference between them, implying that evolution 'couldn't explain it.'
I pointed out that one was a New world primate, the other an Old World primate, separated by at least 40 million years.
He ignored my response for some time, but has now again tried to make it an issue for some reason, by claiming that he needs the "phylo-tree" in order for him to assess it. Funny - he didn't seem to need it when he was trying to declare it a problem for evolution.
Trust me - I am under no illusion that Borger will ever change his mind about anything.
However, his bizarre tactics and conclusions, I think, should be pointed out - repeatedly, if necessary - for the benefit of those that may be fooled by the typical overconfident bluster inherent in so many of the creationist's posts.
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.