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:
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:
<center> <br> <img src="/wiki/download/attachments/4227691/HMM3.png"/> <br> </center>
We highly recommend reading the original HMMER3 documentation to learn how to use utilities provided by the plugin.