Software « Rannala Research Group

Software

Phylogenetics

BYPASSR Package

The BYPASSR and BYPASSRdegr software packages for estimating site-specific rates and degradation levels of ancient DNA sequences, respectively, are available from Ligia Mateiu's web site

MAPminer Package

The MAPminer software for summarizing a posterior distribution of phylogenies is available from Karen Cranston's website

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 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. 2005. In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection. American Journal of Human Genetics 76:1066-1073.
Program Support: Questions about general issues/problems using this program can be directed to ygwang@ucdavis.edu .

Inference of Recent Migration

BayesAss+: Bayesian Inference of Recent Migration 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.
| 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.
Program Support: Questions about general issues/problems using this program can be directed to brannala@ucdavis.edu.

BayesAssNM: Bayesian Inference of Recent Migration Using Multilocus Genotypes (Migrants 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 about general issues/problems using this program can be directed to brannala@ucdavis.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.

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.
Program Support: Questions about general issues/problems using this program can be directed to brannala@ucdavis.edu.

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.
Program Support: Questions about general issues/problems using this program can be directed to brannala@ucdavis.edu.

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.
Program Support: Questions and answers about general issues/problems using this program should be directed to z.yang@ucl.ac.uk.

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.
Reference: E. C. Anderson and P. A. Scheet. 2001. Improving the estimation of bacterial allele frequencies. Genetics 158:1383-1386.
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.
Program Support: Questions about the program should be addressed to eric.anderson@noaa.gov.

Gene Flow Estimation

Maximum Likelihood Estimation of Migration Rates for Wright Island Model

Rannala Research Group Genome Center and Department of Evolution and Ecology, UC Davis