Data matrices and R scripts for the paper “Quantifying environmental adaptation of metabolic pathways in metagenomics”

With respect to your your metagenomics paper which appeared in PNAS (, I was wondering if it is still possible to access the entire (1) environmental features vs. geographic sites and (2) metabolic features vs. geographic sites matricesas used in the paper? Also, is it still possible to access the R scripts that were used in this work?


probe radius


I would like to calculate the solvent accessible surface of certain
proteins. By using your method (online available on one can set the probe radius
to maximal size of 1.6 Å. Because I would like to mimic methylene groups as
solvent, the probe radius should be ~1.9 Å (Johnson R.M. et al, Biochemistry
2006, 45, 8507-8515) .
Is there a possibility to increase the probe size radius to 1.9 Å and
calculate the accessible surface using your method?

Question goes here


Your answer here

I think you can do this by downloading the software from