GC bias is, of course, very important because it can fool both the
algorithms used to generate trees, and most of the methods to
statistically evaluate those trees. However, there are methods to
identify and correct for such bias:
Steel, M. A., Lockhart, P. J., and Penny, D., 1993 Confidence in
evolutionary trees from biological sequence data. Nature 364: 440-442.
Lockhart, P. J., Steel, M. A., Hendy, M. D., and Penny, D., 1994
Recovering evolutionary trees under a more realistic model of sequence
evolution. Molecular Biology and Evolution 11: 605-612.
Chris
