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
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).
hello,
I'm PhD student and I have genomic bacterial data and want to produce a
tree from it. I'm currently using around 10 genomes and I calculated their
"Average Amino acid Identity" so I have the distance matrix
(distance=1-AAI). I produced with ape a neighbor joining tree, and wanted
to
