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

jpHMM [Main page]


jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of recombinations in HIV-1 and hepatitis B virus (HBV) genomes.

For a query sequence phylogenetic recombination breakpoints are predicted and each region of the sequence is assigned to one HIV-1 subtype/HBV genotype. This prediction is based on a pre-calculated multiple alignment of the major HIV-1 subtypes/HBV genotypes. A detailed description of the algorithm and some information about the evaluation can be found here. For information about the output format please see the online submission page.

New application of jpHMM:

Online submission form for jpHMM.

Download the command line version of jpHMM.
Test data sets that were used in the papers can also be found on the download page.

This project is a collaborative effort between the Department of Bioinformatics of the University of Göttingen and the Los Alamos HIV Sequence Database Group.
The application of jpHMM to HBV was developed in collaboration with the Laboratoire INSERM U871 in Lyon and the Laboratoire associé au Centre National de Référence des hépatites B, C et delta, UFR Santé Médecine Biologie Humaine, at the Université Paris 13.

In case of questions concerning jpHMM algorithm details or bugs, please contact For HIV-1 subtyping questions, please contact


Please cite one of the following papers if you use this tool in your publication (a list of all references can be found here):

jpHMM is not actively maintained any longer. (Questions or comments? Email contact)
Copyright © 2005-2006 Dept. of Bioinformatics (IMG)