IPED2 is a method to reconstruct pedigree from genotype data.

IPED2 was created by Dan He

For general questions, comments or suggestions about IPED2, please email Dan He (danhe (AT) cs.ucla.edu, dhe (AT) us.ibm.com).


Download IPED2


To run IPED2, from the command line:

java -jar IPED2.jar -i [num_of_extant_individuals] -d [num_of_generations] -f [ibd_file]

-i: num_of_extant_individuals: the number of extant individuals your data set has.

-d: num_of_generations: the number of generations you want to reconstruct

-f: ibd_file: the input ibd file for the extant individuals. One row for each haplotype of each extant individual. Row 1 and 2 are the two haplotypes for the first individual. Row 3 and 4 are the two haplotypes of the second individual and so on. The haplotypes are divided into chunks at the same positions. Therefore each row is a set of haplotype chunks. Each chunk is assigned an index. Two haplotypes are IBD at the same chunk if they share the same index. In the following example:

1 3 4 9
2 3 4 8

There are two haplotypes, one for each row. Each haplotypes have 4 chunks. They are IBD at the second and third chunks. A pedigree simulator adapted by Zhanyong Wang from the simulator of Bonnie Kirkpatrick is included to generate such ibd files.

output: The reconstructed pedigree. The output file is: pedigree.out. The index of the extant individuals are consistent with the index of the individuals in the ibd_file.


  • v1.1 (2013-10-14) version 1.1 was released.


Dan He, Z Wang, L Parida, E Eskin: IPED2: Inheritance path based algorithm for complicated pedigree reconstruction using genotype data, Submit to ISMB 2014

Please cite the above paper if you are using the IPED2 Software.


For general questions, comments, suggestions, bug report about IPED2, please email Dan He (hedanus (AT) gmail.com, dhe (AT) us.ibm.com).