A brief introduction to HMMBUILD
The program HMMBUILD, belonging to the HMMER package, generates a profile HMM from a multiple sequence alignment. Profile HMMs are statistical models of the primary structure consensus of a sequence family. A profile HMM can typically be used in homology detection by comparing a query profile HMM against a DNA or protein sequence library.
For further details, see the HMMER homepage.

Availability in NPS@
HMMBUILD is available :

First you have to choose the profile HMM construction options :

Then you find the profile HMM calibration options (parameters estimation of an extreme value distribution) : the number of synthetic sequences, the gaussian mean and standard deviation of the synthetic sequence length distribution.

The HMMBUILD output allows you to follow your analysis with a profile HMM search against a protein library thanks to HMMSEARCH.