Statistical Genetics Group Software available

Below is a list of software by members of the Statistical Genetics Group at the University of Reading, plus details of supporting literature if appropriate. Depending on your browser, to download a file either left-click on the name of the program (underlined), or right-click on that name and select the option "Save Target As ...".

Programme for calculating the probability of identification in the presence of given degrees of relatedness in the population, inbreeding and coancestry Contact:
Programme written by: A.D.J. Overall
K.L. Ayres & A.D.J. Overall (2004). API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Molecular Ecology Notes 4, 315-318.
(Updated June 2004, for input problems)
Distributed as: Zipped file containing PC executable, plus test files

Bayesian estimation of the coancestry coefficient FST Contact:
Programme written by: D.J. Balding, K.L. Ayres, M.A. Beaumont, P.O'Reilly
D.J. Balding (2003). Likelihood-based inference for genetic correlation coefficients. Theoretical Population Biology, 63: 221-230
M.A. Beaumont & D.J. Balding (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13: 969-980, 2004
bayesfst.c, INTFILE, myutil.c, myutil.h
Example dataset data_BB04.inp now available (flies data from Beaumont & Balding, 2004)
Further files and R scripts available in the file
Distributed as: ANSI C source code

Bayesian estimation of the population inbreeding coefficient f Contact:
Programme written by: K.L. Ayres
K.L. Ayres & D.J. Balding (1998). Measuring departures from Hardy-Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity 80, 769-777
Description    HWMET.C   HWMET2.C   HWFMET.C   HWMETC.C   HWMETC2.C   FPRIOR.C Distributed as: ANSI C source code

Associated programs from Morris, Whittaker & Curnow (1997) Contact:
Programme written by: A.P. Morris
A. P. Morris, J. C. Whittaker & R. N. Curnow (1997) A likelihood ratio test for detecting patterns of disease-marker association. Annals of Human Genetics 61, 335-350. Distributed as: ZIPPED file

Bayesian estimation of gametic disequilibrium coefficients Contact:
Programme written by: K.L. Ayres
K.L. Ayres & D.J. Balding (2001). Measuring gametic disequilibrium from multi-locus data. Genetics 157, 413 - 423
LDMET.C   LDMET3.C   LDHAP.C   Distributed as: ANSI C source code

A package implementing MCMC sampling of phylogenetic trees using five-state models of nucleotide substitution Contact:
Programme written by: G. McGuire, P.M. Agapow
G. McGuire, M.C. Denham & D. J. Balding (2001) Models of evolution for DNA sequences including gaps Molecular Biology and Evolution 18, 481 - 490
From URL: Distributed as: TAR file, also other Mac and Windows binaries

MCMC sampling of coalescent trees for microsatellite loci Contact:
Programme written by: I.J. Wilson
I. J. Wilson & D. J. Balding (1998) Genealogical inference from microsatellite data. Genetics, 150, 499-510.
From URL: Distributed as: GZIPPED TAR file of C source code

Package for scanning multiple alignments for sporadic recombination events Contact:
Programme written by: G. McGuire
G. McGuire and F. Wright (2000) TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics 16, 130-134.
topal2.03b.tar.Z Distributed as: COMPRESSED TAR file of Unix shell scripts, C and C++ source code

Please note: all software available here remains the intellectual property of the authors, whether copyright is asserted or not. Unless otherwise stated, all programs are provided without guarantee to perform any particular function.

Last updated: Sep. 2008 Site maintained by: Karen Ayres