GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

System requirements

GlimmerHMM is released as source code and was tested on Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any Unix system.


GlimmerHMM has been trained on several species including Arabidopsis thaliana, Coccidioides species, Cryptococcus neoformans, and Brugia malayi.

  Nuc Sens Nuc Spec Nuc Accur Exon Sens Exon Spec Exact Genes Size of test set
Arabidopsis 97% 99% 98% 84% 89% 60% 809 genes
Cryptococcus 96% 99% 98% 86% 88% 53% 350 genes
Coccidioides 99% 99% 99% 84% 86% 60% 503 genes
Brugia 93% 98% 95% 78% 83% 25% 477 genes

Obtaining GlimmerHMM

This software is  OSI Certified Open Source Software .

To download the complete GlimmerHMM system, just click here .

After downloading, uncompress the distribution file by typing:

% tar -xzf GlimmerHMM.tar.gz

A directory named 'GlimmerHMM/' will be created which contains the executable, training data sets, and other supporting files.

Contact Information

Please consult the current GlimmerHMM page for contact information.


1. W.H. Majoros, M. Pertea, and S.L. Salzberg. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders (73K, PDF format)


The development of GlimmerHMM was supported by the NIH under grants R01-LM06845 and R01-LM007938.