The HMM3 plugin is a toolkit based on Sean Eddy’s HMMER3 package.
While working on this plugin we were guided by the following principles:
The current version of UGENE provides a 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 ‣ HMMER 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.