There are a number of new features, including

• For mothur/QIIME users, guppy and rppr can now use a BIOM file and tree in place of a reference package and .jplace file.
• Edge PCA can now perform support overlap minimization (SOM), which minimizes overlap between the first two or three principal components. Note that the guppy pca subcommand has been renamed to guppy epca, and the output file extensions have changed.
• The mean and variance of PD can be calculated using guppy rarefact.
• The alpha diversity measures calculated by guppy fpd now includes the BWPD metric we recently described, as well as support for the qD(T) measure of Chao et. al. (2010).

Plus lots of bugfixes and improvements: see the CHANGELOG for details.

Although we very much wanted a final version of classification code in this release, validation is still ongoing.