The question which Jonathan Wendel raised is really quite important
because it has far-reacing implications on tree building. Indeed,
while the problem is commonly referred to as a lack of stationarity,
it is rarely dealt with.
A set of sequence are said to evolve under stationarity if they have
not experience a change in their composition of chatacters. This is
not easy to determine because we rarely have the ancestral sequence
available. Therefore, if the sequences in question have the same
composition, it is common to assume that the sequences evolved under
Lack of stationarity can occur at both the DNA and protein level (see
PG Foster et al., Journal of Molecular Evolution, in press) and thus
affects phylogenetic analyses of both DNA and protein data.
All the best,
lars.jermiin at anu.edu.au