pid, Version 0.9: Alignment-Free Diversity Computation

Bernhard Haubold Haubold and Peter Pfaffelhuber

pid is a computer program for estimating the number of pairwise mismatches per site between two unaligned DNA sequences. In population genetics this quantity is often referred to as $\pi$. pid implements the estimator $\pi_{\rm d}$ derived by Peter Pfaffelhuber and Bernhard Haubold.

The simulations described in the documentation for pid refer to the program generateQuerySbjct, which in turn requires the following three programs to run:

1. ms
2. macs
3. ms2dna