Free Software

Periodically I will be distributing software we and our collaborators have been developing.

Hugh Salamon, May 1999

The Stanford Center for Tuberculosis Research ProbeBrowser is useful for presentation and analysis of hybridization microarray experimental results. We have found it particularly useful for our genomic DNA data. It should prove useful with RNA hybridization data for expression profiling as well. Version 1.7.0 is available with supplementary data for the May 28th report in Science on BCG vaccine genomics.

ProbeBrowser version 1.7.0 for Windows 95/NT may be downloaded for free.

Stanford Center for Tuberculosis Research Molecular Fingerprint Analyzer J is software which extends SCTR-MFA utilties, providing fingerprint analysis project management, fully automated clustering, genetic distance and nearest genetic distance calculations, queries, and plotting. This package permits fragment length fingerprint data from different typing labs to be compared, by exploiting an analysis of error in replicate typing data from each laboratory. This is work in progress, but we welcome a few testers at this stage.

MFA-J is written in Java and uses native C libraries for some calculations. MFA-J version 2.0 for Windows 95/NT may be obtained from here. If there is significant interest in using this software on other platforms, we will be interested in providing the software for other operating systems.

Please note: MFA-J is not a gel-image analysis program. It imports fragment length estimates exported from gel-image analysis programs.

Questions about the use of this software should be directed to Melvin Javonillo:

Questions regarding development of fingerprint comparison algorithms and software should be directed to Hugh Salamon, now at:

Stanford Center for Tuberculosis Research Molecular Fingerprint Analyzer (SCTR-MFA) version 0.4.3.

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 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 PM. 1998.
         Error Analysis in Comparison and Clustering of Molecular
         Fingerprints. Emerging Infectious Diseases
         (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.

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

You may also obtain software for analysis of sets of aligned sequence data here. MINCOV implements the unique combinations method, defining combinations of variants unique to a sequence with respect to a set of aligned sequences.

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Last updated February 8, 2001