Source code download
The following archive contains all source code files to run the jpHMM locally.
- jpHMM.tar.gz [3.02MB]
Additionally it contains a multiple sequence alignment containing all major HIV-1 subtypes, an example, the required parameter files and a documentation (pdf) of the jpHMM program.
For a detailed description of the algorithm please see Schultz et al. or the Diplom thesis (pdf, German) of A.-K. Schultz. A list of all references can be found here.
Please note: in contrast to the web server output (Online submission) the output of the recombination breakpoints of this command line version is only based on raw sequence positions, not on HXB2 numbering.
In case of questions or bugs please contact jphmm-web@gobics.de.
Last update: May 27th, 2009
Please cite the following paper if you use this program in your publication (a list of all references can be found here):
- A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke. A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes. BMC Bioinformatics 7:265. 2006
- A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM: Improving the reliability of recombination prediction in HIV-1. Nucleic Acids Research, 37:W647-51. 2009
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