The use of the attached source codes is allowed under the terms of the GNU general public license (version 3).

Hippo and AEML

Haplotype estimation using incomplete prior information from pooled observations (Hippo), and
Approximate EM-algorithm with list of known haplotypes (AEML) are in a
Tar-package.
These algorithms try to estimate the population haplotype frequencies from pooled SNP data and can make use of a list of the haplotypes that are known to exist in the population. Written in ANSI-C using Gnu Scientific Library (GSL v.1.0.0). For description see:

Pirinen M (2009):
Estimating population haplotype frequencies from pooled SNP data using incomplete prior information.
Bioinformatics (accepted).

APE

Allelic Path Explorer (APE)
As a Tar-package.
APE is a program for extending partially known genotype data on a given pedigree consistently (i.e. in accordance with the Mendelian rules) to the whole pedigree. Written in ANSI-C. For details, see:

Pirinen M and Gasbarra D (2006):
Finding Consistent Gene Transmission Patterns on Large and Complex Pedigrees.
IEEE/ACM Trans. on Computational Biology and Bioinformatics vol.3 no.3:252-262