Software for Molecular Epidmiology
hugh at molepi.stanford.edu
Wed May 13 11:13:26 EST 1998
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
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
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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