Under each directory, there is a README file. Please read the README file before reading the files.

dpph: The source code of DPPH. (including detailed comments)

graph_realization: The source code of the graph realization. (including detailed comments)

pph_step: The program reads one row in each run and shows how the output and tree change when each row is added.

xhudson: A modified Hudson program which extracts the recombindation points and also can generate the mutations under certain percentage.

gpph: The source code of GPPH. (including detailed comments)

hpph: The source code of HPPH

pphs: A program which can find intervals which have unique solutions when the input data has recombinations. (DPPH is used to find the unique solutions in each interval)

large: This program can read a very large genotype file and find PPH solutions for 30 site intervals starting from each site.

percent: The program does the experiments of the phase transitions.

test_data: The test data for three PPH programs in the paper: 
           "Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers"