HMMER

HMMER is a software suite for making and using Hidden Markov Models (HMMs) of biological sequences.

Installed on the Opteron Cluster.

Opteron cluster Version 2.3.2

It is convenient to use /biomed/lib/examples/.login.fixed for this and other sequence analysis packages.

Nine programs are available in /biomed/bin, as listed below. The links for each will take you to the appropriate man page.

  • hmmalign, aligns sequences to an HMM profile.
  • hmmbuild, build a hidden Markov model from an alignment.
    Example job
  • hmmcalibrate, calibrate HMM search statistics.
  • hmmconvert, convert between profile HMM file formats.
  • hmmemit, generate sequences from a profile HMM.
  • hmmfetch, retrieve specific HMM from an HMM database.
  • hmmindex, create SSI index for an HMM database.
  • hmmpfam, search one or more sequences against HMM database.
  • hmmsearch, search a sequence database with a profile HMM.

Or, see the general man page for hmmer.

Short descriptions, arguments and switches for the nine programs are displayed by typing:

 /biomed/bin/program-name -h

HMMER Documentation:

See also: