Heu-MCHC is a fast and accurate heuristic algorithm for the Minimum-Change Haplotype Configuration (MCHC) problem, i.e. a combinatorial formulation of the haplotype inference problem on pedigree data where the total number of recombinations and point mutations has to be minimized.
Heu-MCHC has been designed and implemented by Yuri Pirola under the supervision of Tao Jiang.
Reference
Please cite the following paper when using Heu-MCHC:
Yuri Pirola, Paola Bonizzoni, and Tao Jiang. An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear (2011). doi:10.1109/TCBB.2011.51
A preliminary version of this work entitled Haplotype inference on pedigrees with recombinations and mutations appeared in Proceedings of the 10th International Workshop on Algorithms in Bioinformatics (WABI), LNBI 6293, pp. 148-161. Springer, Heidelberg (2010). doi:10.1007/978-3-642-15294-8_13
(A pre-print version is available upon request to one of the authors.)
Availability
Heu-MCHC is released under the GNU General Public License version 3 or later.
The source code is freely available at the git repository located at https://github.com/yp/Heu-MCHC. The latest stable version is v1.0.1 (February 24, 2011).
For your convenience, we also provide a binary distribution for Linux 64-bit operating systems (fully tested and supported on Ubuntu 10.04 x64) of the latest stable version.
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Linux (64-bit), .tar.gz format 7.7MB
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Linux (64-bit), .tar.bz2 format 7.3MB
Technical documentation and examples are included in the distribution packages and can be browsed online at the project GitHub page. Please refer to the publication cited above for the description of the heuristic method.
Contacts
Please contact Yuri Pirola for additional information.
