NAME

       Algorithm::HMM - Perl bindings for a Hidden Markov Model library.

SYNOPSIS

         use Algorithm::HMM;

         # Load a Hidden Markov Model.
         my $hmm = new Algorithm::HMM(Model => 'sample.hmm');

         # Run a sequence through the loaded model.
         my $rep = $hmm->search("AAIELKBPOWELKQJPASDLKJIGE");

         # Get all the global hits from the search.
         my @ghits = $rep->global_hits();

         # Get all the domain hits from the search.
         my @dhits = $rep->domain_hits();

         # Display information about the domain hits.
         for (@dhits) {
           print("pvalue = " . $_->pvalue . "\n");
           print("evalue = " . $_->evalue . "\n");
           print("score  = " . $_->score  . "\n");
         }

         # Save the model to a different file.
         $hmm->save("sample.hmm.0");

         # Load the saved model again.
         $hmm->load("sample.hmm.1")