What are the licenses?
The programs and source codes are released under a variety of software license agreements, depending on which institutions were involved in financing the work.
Most of this software is free for academic use, although not all of it is open source. Please check the license that comes with the package to be sure that you respect the agreements.
HaploPool -- a program for estimating haplotype frequencies from genotypes
PhyloPed -- a program for phasing individuals in a family
COP and CIP -- C++ programs for predicting family relationships among extant individuals
TreePopping -- a C++ program implementing a perfect phylogeny reconstruction algorithm for binary data with missing values