Source code download
The following archives contain all source code files to run jpHMM locally. It also includes the newly implemented circular version of jpHMM.
- jpHMM source code (Mar 2015): jpHMM.tar.gz [52MB]
- Matlab code for estimating the emission probabilities by linear classifier learning (Bulla et al., 2012): matlab.zip [29KB]
- Code for estimating the emission probabilities using a model-based information sharing protocol: src.zip [50KB]
Additionally the archives contain multiple sequence alignments for HIV-1, HCV and HBV, an example, the required parameter files and a documentation (pdf) of the jpHMM program.
Test data download
The following archives contain the test data for the application of jpHMM to HIV-1 and HBV.
For a detailed description of the algorithm please see Schultz et al., 2006, or the PhD (pdf) or Diplom thesis (pdf, German) of A.-K. Schultz. A list of all references can be found here.
For the application to HIV, 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 firstname.lastname@example.org.
Last update: August 1st, 2012
Please cite one of the following papers if you use this program in your publication (a list of all references can be found here):
- A.-K. Schultz, I. Bulla, M. Abdou-Chekaraou, E. Gordien, B. Morgenstern, F. Zoulim, P. Dény, M. Stanke. jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Research, 40:W193-W198. 2012.
- 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
- 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
- M. Zhang, A.-K. Schultz, C. Calef, C. Kuiken, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res., 34:W463-5. 2006.
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