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HMMER container

Main tool : HMMER

Code repository: https://github.com/EddyRivasLab/hmmer

Basic information on how to use this tool:

  • executables:

    • alimask
    • hmmalign
    • hmmbuild
    • hmmconvert
    • hmmemit
    • hmmfetch
    • hmmlogo
    • hmmpgmd
    • hmmpgmd_shard
    • hmmpress
    • hmmscan
    • hmmsearch
    • hmmsim
    • hmmstat
    • jackhmmer
    • makehmmerdb
    • nhmmer
    • nhmmscan
    • phmmer

  • help: -h

  • version: -v

  • description:

HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs).

Full documentation: http://eddylab.org/software/hmmer/Userguide.pdf

Example commands

# build a profile from an alignment
hmmbuild hmm_file msa_file

# search profile against a sequence database
hmmsearch hmm_file seqs.fa