I have a set of orthologous sequences of approximately 150 amino acids
from ten different animal species. The sequences don't differ very
much, most of them in about ten positions.
I have made maximum parsimony and neighbor-joining trees with these
sequences, which are looking quite nicely, but how can I say
anything about the reliability of these trees?
Bootstrapping would clearly not be of much use, since in the
resampling process often all significant sites will be removed.
Or do I just have to accept that trees based on such small data sets
will never be very reliable?
Any suggestions will be appreciated.
University of Nijmegen
gertjan at sci.kun.nl