New: Version 2.1 has been released. The new version supports abundance-weighted calculations of standardized indices and p-values of several alpha diversity measures, using different null models. Check the documentation section and download the new version from CRAN. 

PhyloMeasures is an R package that provides fast computations of phylogenetic biodiversity measures.The package functions can process large phylogenetic data in just a few seconds on standard computers.

PhyloMeasures provides functions for computing the standardized values and p-values of several phylogenetic biodiversity measures. The measures which are supported in the current version of the package are: the Phylogenetic Diversity (PD), the Mean Pairwise Distance (MPD), the Mean Nearest Taxon Distance (MNTD), the Core Ancestor Cost (CAC), the Common Branch Length (CBL), the Community Distance (CD), the Community Distance Nearest Taxon (CDNT), the Phylogenetic Sorensen's Similarity (PhyloSor), and the Unique Fraction (UniFrac).

The main advantages of PhyloMeasures are: 
1) The package provides exact computation of the standardized indices and p-values for several phylogenetic biodiversity measures.

2) All functions provided in PhyloMeasures are designed to be very efficient in practice, and they can process in a few seconds even trees that consist of several hundred thousand tips.  The package functions are developed based on standard techniques in Algorithms Design, hence their performance scales ideally as the size of the input trees increases.

As of version 2.1, the package uses a novel technique, called Incremental Monte Carlo, that speeds up substantially null model computations for p-values and standardized indices. This technique can be used for speeding up all kinds of batched biodiversity computations (i.e. not only phylogenetic ones)  that require maintaining species richness.  A scientific article that describes the new technique is soon to be published.
 You can download PhyloMeasures from CRAN; you can do this by clicking on the Download tab on this page.