Supported Applications


  • Description

    an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

  • Primary Citation*

    M. Remmert, A. Biegert, A. Hauser, and J. Söding. 2012. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods. 9: 173-175.

    • *Full citation information available through

  • Citation Note

    Please cite the following url:

  • Keywords

    High-throughput sequencing, Proteomics

  • Default Versions

    Linux 64:  3.0.3
    OS X INTEL:  3.0.3

  • Other Available Versions

      Linux 64:

    • OS X INTEL:

  • Developers

    Johannes Soeding, Martin Steinegger.