Software for Molecular Epidmiology

Hugh Salamon hugh at molepi.stanford.edu
Wed May 13 11:13:26 EST 1998


This announcement can be found at
http://molepi.stanford.edu/free_software.html.

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
maps), 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
at                                          
     http://www.cdc.gov/ncidod/EID/vol4no2/salamon.htm) 

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:
http://molepi.stanford.edu/hugh/mfa/readme.html.




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