Phylogenetic Beta-Diversity In Picante

Question

[otk]

I am calculating inter-sample phylogenetic distance. There are functions comdist and comdistnt in Phylocom, which can also be used with randomizations / null-model testing of observed patterns (option -n). For certain reasons I cannot use Phylocom (for one, it crashes on my data). I would rather use R. There are similar functions in picante package, but they do not allow for null-model testing. Is there a way to implement it in R? Maybe with a script/wrapper around comdist functions?

Answer 1

[Josh Herr]

Have you tried UniFrac for assessing diversity through branch lengths? I'm not aware of any R scripts but wouldn't be surprised if they exist.