Authors of software components

PyPop

Alex Lancaster (alexl at users.sourceforge.net)

    Co-designer of Python framework: author of main engine, text file parser,
    Python extension module framework using SWIG, XML output and XSLT
    post-processing framework (to generate plain text and HTML output).

Mark P. Nelson

    Co-designer of Python framework: implemented and maintained Python modules,
    particularly the module for Hardy-Weinberg analysis. Updated and maintained
    XSLT code.

Richard M. Single (Richard.Single at uvm.edu)

    Author of haplotype frequency and linkage disequilibrium analysis module
    "emhaplofreq", author of R programs to do further statistical analysis and
    generate graphs and figures in PostScript.

Diogo Meyer (diogo at ib.usp.br)

    Contributed further statistical analysis code for the R programs.

Owen Solberg (solberg at berkeley.edu)

    Implemented filter modules, including conversion to allele name information
    to sequence data.

Yingssu Tsai

    Implemented prototype of the allele names to sequence conversion filter
    module.

Glenys Thomson (glenys at berkeley.edu)

    Principal investigator and project lead.

Third-party modules

gthwe

    The Hardy-Weinberg "exact test" implementation is a modified version of Guo
    & Thompson's [Guo:Thompson:1992?] code. Dr. Sun-Wei Guo has kindly allowed
    us to release the code under the GNU General Public License. Original code
    available at http://www.stat.washington.edu/thompson/Genepi/Hardy.shtml.

slatkin-exact/monte-carlo.c

    Montgomery Slatkin's implementation of a Monte Carlo approximation of the
    Ewens-Watterson exact test of neutrality ([Slatkin:1994?],
    [Slatkin:1996?]). Original code can be found at: http://ib.berkeley.edu/
    labs/slatkin/monty/Ewens_exact.program.

pval

    The code in the '"pval"' directory (with the exception of '"pval.c"' the
    SWIG wrapper, "'pval_wrap.i"' and the Makefile) is part of the R project's
    'nmath' numerical library http://www.r-project.org/ and is also licensed
    under the GNU General Public License (GPL). Minor modifications have been
    made to allow the module to build correctly.

Acknowlegements

This work has benefited from the support of NIH grant AI49213 (13th IHW).
Thanks to Steven J. Mack, Kristie A. Mather, Steven G.E. Marsh and Leslie Louie
for helpful comments and testing.

