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 buildHMM3 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:

     <img src="/wiki/download/attachments/54363788/HMM2.png"/>

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