Salvador Espada Hinojosa --
The problem, of course, is that a random substitution on an interior
branch of a tree increases or decreases the size of more than one
distance in the distance matrix. The distances aren't independent in
their statistical noise. So you can't just sample distances afte
Hi Salvador,
You first need to define the variables that would be resampled during
the bootstrap procedure. In the case of DNA sequences, this would be the
columns (= sites) of the alignment, since they each contribute to the
distance calculation (or to the likelihod function if you use ML). S