tax2tree

tax2tree is a tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P; ISME J., 2012; doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.

http://tax2tree.sourceforge.net