search for: phylometric

...f the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in microbial ecology (if not outright theoretically false). What I have instead is a phylometric distance matrix between all my samples based on a phylogenetic tree. Some people have apparently made such a python implementation <http://qiime.org/scripts/compare_categories.html>, but I'd rather use R. Thanks in advance, Roey