The HMM3 plugin is a toolkit based on the Sean Eddy’s HMMER3 package.

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

• Make the HMMER3 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 HMMER3 package.
• Create the high-performance solution utilizing modern multi-core processors.

The current version of UGENE provides user interface for three HMM3 tools: HMM3 build, HMM3 search and Phmmer search.

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

To access these tools select the Tools ‣ HMMER3 tools submenu of the program main menu:

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We highly recommend reading the original HMMER3 documentation to learn how to use utilities provided by the plugin.