University of Göttingen  |  Faculty of Biology  |  Institute of Microbiology and Genetics  |  Dept. of Bioinformatics

jpHMM [Download]

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.

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

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):

Questions or comments? Email contact
Copyright © 2005-2006 Dept. of Bioinformatics (IMG)