Software from the Rannala Research Group

Gene Mapping and Allele Age Estimation

DMLE+: Multipoint Linkage Disequilibrium Mapping.

All versions of the DMLE/DMLE+ program are now distributed from dmle.org.

GeneArtisan: Simulation of Genetic Markers in Case-Control Study Designs.

Version 1.1 Release Date 22 May 2005. Note: This release implements an improved algorithm for simulating samples that allows larger intervals to be used and dramatically improves execution time. Check this page for updates and bug reports.

|Linux GUI (v1.0)| Mac OS X GUI| Linux Terminal| Mac OS X Terminal| Windows Terminal| Source Code (Terminal)| Source Code (GUI)|

Reference: Y.Wang and B. Rannala 2003. In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection. American Journal of Human Genetics 76 (In Press).

Program Support: Questions and answers about general issues/problems using this program should be posted to the Genetics Software Forum (http://rannala.org/gsf). Bugs causing program crashes etc should be reported to ygwang@ucdavis.edu .

Inference of Recent Migration

BayesAss+: Bayesian Estimation of Recent Migration Rates Using Multilocus Genotypes.

Version 1.3 Release Date 4 May 2005. Note: New feature was added to output the 95% credible interval for the migration rate estimates. This is helpful in determining when the marker data are informative about migration by comparing the resulting posterior credible intervals with those expected under the prior (e.g., when the data are completely uninformative). Only the Windows release of version 1.3 is currently available. Releases for other operating systems will be posted soon.

|Linux (v.1.2)| Mac OS X (v.1.2)| Windows (v.1.3)| Source Code (v.1.2)| Documentation (v.1.3)| Input File|

Reference: G.A. Wilson and B. Rannala 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191. Reprint(PDF format for Adobe Acrobat)

Program Support: Questions and answers about general issues/problems using this program should be posted to the Genetics Software Forum (http://rannala.org/gsf). Bugs causing program crashes etc should be reported to gregwils@uclink.berkeley.edu .

BayesAssNM: Bayesian Estimation of Recent Migration Rates Using Multilocus Genotypes When Migrants Are Not Included In the Sample.

Version 1.0 Release Date 21 January 2005 Note: This version of BayesAss is only to be used when genotypes are obtained from samples that are known not to be migrants, such as embryos.

Linux Source Code Documentation

Reference: Jehle R, GA Wilson, JW Arntzen, and T Burke. 2005. Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus). Journal of Evolutionary Biology (In Press).

Program Support: Questions and answers about general issues/problems using this program should be posted to the Genetics Software Forum (http://rannala.org/gsf). Bugs causing program crashes etc should be reported to gregwils@uclink.berkeley.edu .

BayesAss- : Bayesian Population Assignment of Haploid Organisms Using Multilocus Genotypes.

Version 1.0 Release Date 18 July 2002 (Beta).

|Windows 95/98/NT |Mac Classic OS |Mac OS X |Input File |

Reference: M.C. Fisher, B. Rannala, V. Chaturvedi and J.W. Taylor. 2002. Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human Coccidioides infections. Proceedings of the National Academy of Sciences USA 99:9067-9071. Reprint(PDF format for Adobe Acrobat)

Immanc: Detecting Immigrants Using Multilocus Genotypes.

Version 5.0. Release Date 8 Oct 1998.

Windows 95/98/NT|Linux i386 |Mac OS X |Mac Classic |Documentation|Input File|

Reference: Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 94: 9197-9201. Reprint(PDF format for Adobe Acrobat)

BDMC21: Maximum Likelihood Estimation of Allele Ages. Version 2.1.

Release Date 7 Oct 1998.

|Windows 95/98/NT|Linux i386|Documentation|Input File|

Reference: Slatkin, M., and B. Rannala. 1997. Estimating the age of alleles by use of intraallelic variability. American Journal of Human Genetics 60: 447-458.

Mutational Analysis of Cancers

oncSpectrum : Likelihood Analysis of the Spectrum of Somatic Mutations in Cancers.

Version 1.0 Release Date 2 Mar 2004. oncSpectrum_v1_tar.gz (Windows executable, source code, example input files, and documentation)

Reference: Z. Yang, S. Ro and B. Rannala. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165: 695-705. Reprint(PDF format for Adobe Acrobat )

Inference of Allele Frequencies in Microbial Populations

BACTFREQ: Maximum Likelihood Estimation of Bacterial Allele Frequencies (replaces BFREQ program).

Program by Eric Anderson (Univ. Washington), Release Date 10 June 2001.

|Windows 95/98/NT |Macintosh |Source Code in C |

Users of this program are requested to cite both the papers listed below. Questions about the program should be addressed to eriq@u.washington.edu .

Reference: E. C. Anderson and P. A. Scheet. 2001. Improving the estimation of bacterial allele frequencies. Genetics (July, to appear).

Reference: B. Rannala, W. Qui, and D. E. Dykhuizen. 2000. Methods for estimating gene frequencies and detecting selection in bacterial populations. Genetics 155: 499-508. Reprint(PDF format for Adobe Acrobat)

Gene Flow Estimation

Maximum Likelihood Estimation of Migration Rates for Wright Island Model.

|Windows 95/98/NT |Linux i386 |Documentation |Input File |

Reference: Rannala, B., and J. A. Hartigan. 1996. Estimating gene flow in island populations. Genetical Research 67:147-158. (Read Abstract On-line) BayesAss

Pending Releases

BayesAss version 2.0

BA2 will be available soon. The partially completed manual provides a preview of the features that will be available in the new release.

BayesAss 2.0: BA2 Users Guide