multi_hmmsearch(1) perform a hmmsearch into multiple FASTA files using


multi_hmmsearch -p hmm_file [-i] -f index_file


Not technically a Bio::Tools::Run script as this doesn't use any Bioperl or Bioperl-run components but it's useful.

Mandatory Options:

  -p  HMM profile to use for the search.
  -f  INDEX file that contains a list of FASTA files for the multiple

Special Options:

  -i  Create a new index file with the resulting hmms files. This is
      useful if you want to pass this list as input arguments into
      another programs.
  -h  Show this documentation.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


  Mauricio Herrera Cuadra <>