The HMM3 build tool is used to build a new HMM profile from a multiple alignment. You can use any alignment file formats supported by UGENE.
The output HMM profile format is compatible with the HMMER3 package, but it is not compatible with the HMMER2.
The HMM3 build automatically calibrates the target model.
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The HMM3 configuration dialog provides an easy way to set appropriate search parameters.
Here you can see effective weighting strategies options:
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