Software for Molecular Epidemiology

Lauri Henttonen in CA lauri.henttonen at satama.com
Wed May 13 11:01:35 EST 1998

The following software may be of general interest to some
This announcement can be found at

Beta Testers Wanted for Stanford Center for 
Tuberculosis Research Molecular Fingerprint Analyzer
(SCTR-MFA) version 0.4.2! 

SCTR-MFA runs an error analysis program on replicate strain fingerprint 
data, which in turn recommends a method to compare lanes, and calculates 
parameter values to use with comparison methods. SCTR-MFA also
includes programs to compare fragment length data using one of 
two methods (Align-and-Count or Interpolated Error), calculate 
genetic distances, and create lists of clustered fingerprints 
(a number of rules are provided). SCTR-MFA is extensible to 
include third-party or user-developed comparison methods,
genetic distance calculators, and clustering rule programs. 

SCTR-MFA does not currently present data visually (e.g., with lane
nor does it perform cluster refinement. The following reference 
describes the Align-and-Count Method, introduces the clustering
approach used by the software, and describes cluster refinement: 

     Salamon H, Segal MR, Ponce de Leon A, Small P. Error Analysis 
     Facilitates Comparison and Clustering of Molecular Fingerprints. 
     Emerging Infectious Diseases 
     Vol. 2 No. 4 Apr-Jun 1998. (Online version available

Please register and download SCTR-MFA if you would like to test 
this software for Windows 95/NT. If you would like the command 
line programs (which perform all the analyses) for Unix
operating systems, please email me hugh at molepi.stanford.edu. 

Here is the documentation distributed with SCTR-MFA version 0.4.1:

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