The following programs have been developed over the course of my career to facilitate analyses of genetic data for a wide variety of research topics.  Please feel free to contact me at any time if you have questions or comments about my software packages (see contact information below).  Suggestions for features that could be included in future releases are always welcomed!

Note:  Mark is employed by the U.S. Geological Survey.  The contents of this web site do not reflect any particular endorsement by the U.S. Government.

Mark can now be reached at markperrymiller@gmail.com


Click on the highlighted text for instructions on downloading each program.

ALLELES IN SPACE (AIS)
A computer program for the joint analysis of inter-individual spatial and genetic information.  This program performs a variety of spatial analyses with genetic data including:  Mantel Tests, Spatial Autocorrelation Analyses, Allelic Aggregation Index Analyses (AAIA), Mommonier's Algorithm, and "Genetic Landscape Shape" interpolations (Click here to see some examples of graphical outputs produced by the program).  Please refer to Journal of Heredity 96: 722-723 (2005) for more information.

TFPGA
Tools for Population Genetic Analyses: A Windows program for the analysis of allozyme and molecular population genetic data. This program calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. Additional features include the ability to analyze hierarchical data sets as well as data from either codominant markers such as allozymes or dominant markers such as AFLPs or RAPDs.

RxC
R by C: A program that performs Fisher's Exact test on any sized contingency table through the use of the Metropolis algorithm

MANTEL-STRUCT
A program that tests for population structure through the use of Mantel Tests. Please refer to Journal of Heredity 90: 258-259 (1999). NOTE: This program does NOT perform standard matrix correlation analyses.

AMOVA-PREP
This program reads raw data sets and prepares all input files needed for use with Laurent Excoffier's WINAMOVA program. It is intended only for use with dominant marker data such as AFLPs or RAPDs.

CIST
Confidence Intervals for Sage Tags:  A Windows program for the analysis of gene expression data generated using SAGE (Serial Analysis of Gene Expression).


 

 

 

 

 

 

 

 

 

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