Re: [R-sig-phylo] Average Aminoacid Identity tree with bootstrap support. Is it possible?

2017-04-07 Thread Joe Felsenstein
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

Re: [R-sig-phylo] Average Aminoacid Identity tree with bootstrap support. Is it possible?

2017-04-07 Thread Emmanuel Paradis
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).