One thing that current phylogeny packages do not do is alignments. It
is clearly unrealistic to expect that nucleotide sequences from a large
number of species can be properly aligned _before_ the phylogeny has
been estimated, but that is what all the packages assume. As available
computing power increases, I think we should start to look at ways to
combine alignment and phylogeny estimation.
Jotun Hein has begun to address this issue, by a reciprocal
align - parsimony tree - align - tree etc. algorithm. We have tried to
use his program on some of Larry Abele's decapod rDNA data, and the
alignment looked OK at the end, but the phylogeny didn't make any sense
compared to anything else that had been done with the same data. (We
also haven't had any luck contacting Hein, if anyone knows a reliable
means to get in touch with him via e-mail, please let me know).
While a maximum likelihood method which estimates both alignment and
phylogeny simultaneously is no doubt possible, the calculations are
probably beyond even Crays for now. I think that a reciprocal
parsimony-based alignment, likelihood-based phylogeny program would be a
help.
Ron DeBry
debry at ds1.scri.fsu.edudebry at fsu (BitNet)
