Sequence Alignment and Modeling System

This is the distribution page for the SAM software suite.

We also have a WWW server for using SAM

The SAM distribution is subject to a license agreement. If you are a college, university, or U.S. government lab, downloading the SAM software indicates that you agree to the conditions of the license agreement. Otherwise, please request more information from

Machine classes currently supported include:

The sae and hmmedit programs are available without license agreement either in binary form or source code. These are not updated, and not available in binary form for all platforms.
The creation and distribution of SAM has been supported in part by NSF grants CDA-9115268, IRI-9123692, DBI-9408579 and DBI-9808007; ONR grant N00014-91-J-1162; NIH grants GM17129 and 1 R01 GM068570-01; DOE grant DE-FG03-95ER62112; a grant from the Danish Natural Science Research Council; and the UCSC Center for Biomolecular Science and Engineering;
UCSC Computational Biology Group