Alleles and phylogenetic results

[Ken Kinman]

Dear All,
     When two alleles of a gene are present in a taxon, their divergent differences shouldn't be too problematic for phylogenetic analysis if (1) they haven't diverged very much (differences are small in a large sequence); and/or (2) these two alleles are actually recognized as such.

      However, what if different gene sequences deposited in the NCBI database are different alleles, are NOT recognized as such, and are significantly different?  Does this not have the potential to lead to false conclusions, especially when taxon sampling is still pretty sparse?  I wonder how widespread this problem could be.
   ---Cheers,
          Ken Kinman