cnF2freq (originally same-Chromosome N-loci F2 FREQuencies) is our experimental codebase for analyzing genotype data with a known pedigree structure in different ways. The code has been used to compute line-origin probabilities in outbred and inbred F2 lines, determine phasing (haplotypes) of markers in different pedigree structures, (re)compute sex-specific marker distances based on the Haldane mapping function, and computing the most probable genotype assignments for missing markers as a form of genotyep imputation in pedigrees.

The code exists in several editions tailored for different datasets and experiments. A specific fork for only computing line genotype probabilities is in the process of being released as an R software package.

The edition adapted for the 14th QTL-MAS workshop is available here (doing haplotyping with known genotypes in a multi-generational pedigree, tested support for recomputing marker maps but disabled in this specific version, parallel with OpenMP as well as MPI).

The edition adapted for the 15th QTL-MAS workshop is available here (doing haplotyping and genotype reconstruction with parental genotype data purposefully removed, including code for comparing results against those from Merlin, parallelization with MPI not enabled).

The boost library of a recent release is required. Recommended compilers are the Intel C++ compiler, g++, or Visual C++ 9 or later. Please contact the author for a cleaner version of the code, rather than the specific editions used for published experiments, or pointers regarding building and compiling the code.