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The HMM2 plugin is a toolkit based on the Sean Eddy’s HMMER2 package.

While working on this plugin we were guided by the following principles:

  • Make the HMMER2 tools accessible to a wider user audience by providing graphical interface for all supported utilities for most of the platforms.
  • Be compatible with the original HMMER2 package.
  • Create the high-performance solution utilizing modern multi-core processors and SIMD instructions.

The current version of UGENE provides user interface for three HMM2 tools: HMM buildHMM calibrate and HMM search.

In the original program the corresponding commands are: “hmmbuild”, “hmmcalibrate” and “hmmsearch”.

To access these tools select the Tools ‣ HMMER2 tools submenu of the program main menu:



We highly recommend reading the original HMMER2 documentation to learn how to use utilities provided by the plugin.

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SSE2 algorithm is implemented by Leonid Konyaev, Novosibirsk State University. Use of the SSE2 optimized version of the HMM search algorithm with quad-core CPU gives >30x performance boost when compared with the original single-threaded algorithm (single sequence mode).

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