Software

Title - Name

AMOVA

Highlights

Analysis of Molecular Variance (AMOVA) is a method for studying molecular variation within a species. Electrophoresis, one of the most widely used methods for studying the structure of DNA, produces data of the form of 0s and 1s where 1 denotes the presence of a band and zero its absence. AMOVA works on such data to create a distance matrix between samples in order to measure the genetic structure of the population from which the samples are drawn. In statistical terms, AMOVA is a testing procedure based on permutation analysis and involves few assumptions about the statistical properties of the data.

Contact

G.R. Bishop (gbishop@stats.adelaide.edu.au )

URL address

http://www.bioss.ac.uk/smart/unix/mamova/
slides/frames.htm

Title - Name

AN ALPHABETIC LIST OF GENETIC ANALYSIS SOFTWARE

Highlights

This list contains references and links to computer software, manly on genetic linkage analysis, marker mapping, linkage disequilibrium mapping, and pedigree drawing. The list is offered as a service to the linkage analysis community.

URL address

http://linkage.rockefeller.edu/soft/

Title - Name

ANIMAL BREEDING – AN INTRODUCTORY TUTORIAL

Highlights

The tutorial introduces students to Selection, Multiple traits and Inbreeding. The tutorial reviews the use of selection as a tool in genetic improvement and the factors that influence response to selection in a livestock improvement programme. Multiple traits covers the genetic and phenotypic relationship between traits, correlated response to selection and selection methods for the improvement of multiple traits. Inbreeding introduces the concept of inbreeding and explores the concepts of inbreeding at both a population and an individual animal level. The approach is that of a tutorial that allows the student to explore the important concepts of quantitative genetics. The students understanding of these concepts can be tested by interactive exercices using the simulation software GENUP (developed by Brian Kinghorn, University of New England, Australia), which is supplied with Animal Breeding.

Contact

MacRobert Building, Centre for Land Use and Environmental Sciences (CLUES), King’s College, University of Aberdeen, AB24 5UA E-mail: CLUES@abdn.ac.uk

URL address

http://www.clues.abdn.ac.uk:8080/directory/
Animal/Animal05.html

Title - Name

APIIS (ADAPTABLE PLATFORM INDEPENDENT INFORMATION SYSTEM )

Highlights

Across species information system for creating integrated databases for any animal recording system. The focus is on individual animal records, as well as other information required for herd management and production control. The system design covers the complete range from small on-farm systems to large national systems. A reference pig database is provided, which can be used as a starting point to create a new database. The software is put into the Open Source, i.e. free of licensing fee.

Contact

Eidert Groeneveld, Federal Agricultural Research Centre (FAL), Institute for Animal Breeding, 31535 NEUSTADT-MARIENSEE, Germany, FAX: +49 (0)5034 / 871 143. E-mail: Eildert.Groeneveld@fal.de

URL address

http://apiis.tzv.fal.de/index.pl

Title - Name

ARLEQUIN

Highlights

Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analysing conventional genetic data (standard multi-locus data or mere allele frequency data). A variety of population genetics methods have been implemented either at the intra-population or at the inter-population level, and they can be conveniently selected and parameterised through a graphical interface.

Contact

Laurent Excoffier (laurent.excoffier@zoo.unibe.ch

URL address

http://lgb.unige.ch/arlequin/

Title - Name

ASREML

Highlights

ASReml is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML). Linear mixed effects models provide a rich and flexible tool for the analysis of many data sets commonly arising in the agricultural, biological, medical and environmental sciences. Typical applications include the analysis of (un)balanced longitudinal data, repeated measures analysis, the analysis of (un)balanced designed experiments, the analysis of multi-environment trials, the analysis of both univariate and multivariate animal breeding and genetics data and the analysis of regular or irregular spatial data. ASReml provides a stable platform for delivering well established procedures while also delivering current research in the application of linear mixed models. The strength of ASReml is the use of the Average Information (AI) algorithm and sparse matrix methods for fitting the linear mixed model.

Contact

arthur.gilmour@DPI.NSW.GOV.AU

URL address

http://www.genstat.com/products/asreml/

Title - Name

BEEF SPECIALIST

Highlights

With the BEEF SPECIALIST, Datag have designed a system that not only keeps track of the Beef premium and C.I.D system but also benefits the business by providing detailed information on every aspect of the beef unit, from veterinary records and weight tracking to individual animal margins at slaughter. Information is saved as it is being entered and facilities are made within the program for full back-ups thus ensuring data security. Datag software is easy to use so no training is usually necessary, if however training is required it can be obtained from the company.

Contact

Farm Computer Systems, Blackmoss Farm, Blackmoss Road, Dunham Massey, Altrincham Cheshire WA 14 5RG

URL address

http://www.clues.abdn.ac.uk:8080/directory/
Animal/Animal07.html

Title - Name

BLUPF90 FAMILY OF PROGRAMS

Highlights

The BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding. The goal of the software is to be as simple as with a matrix package and as efficient as in a programming language. For general description, see e.g. a paper from the CCB'99 workshop (link at the program website).

Contact

Ignacy Misztal, Univ of Georgia, Dept Animal and Dairy Science, Athens, GA 30605, USA. Fax: (706) 583-0274. E-mail: ignacy@uga.edu

URL address

http://nce.ads.uga.edu/~ignacy/newprograms.html

Title - Name

CBE – CROSSBREEDING EFFECTS

Highlights

The program package CBE (Crossbreeding Effects) is used for estimation of crossbreeding effects from a great variety of data structures (experimental designs). Maternal, paternal, grandmaternal and cytoplasmic effects can be estimated, if the appropriate genetic groups are available. A detailed analysis of epistatic effects is possible not only for crossbreeding plans with two, but also for crossbreeding plans with more than two source populations.

Contact

Jochen Wolf (e-mail: wolf@vuzv.cz
or:wolf@tzv.fal.de )

URL address

http://www.boku.ac.at/nuwi/software/softcbe.htm

Title - Name

COALESCE 

Highlights

COALESCE estimates the effective population size of a single constant population using non-recombining sequences. It fits the model which has a single population of constant size, and estimates 4Nu, where N is the effective population size and u is the neutral mutation rate per site.

Contact

Mary K. Kuhner, Jon Yamato, Department of Genetics, University of Washington, Box 357360, Seattle, WA 98195-7360, USA E-mail: mkkuhner@genetics.washington.edu

URL address

http://evolution.genetics.washington.edu/
lamarc/coalesce.html

Title - Name

COWGAME

Highlights

Cowgame is a beef herd genetic simulation program. The player starts with a fifty cow herd and makes selections based upon weaning weight, feedlot gain or yearling weight. The next year's calf crop is generated during each session and the genetic information is saved so that future selections can be made. AI sires can also be used.

Contact

Burditt, Buchanan (Oklahoma State University) E-mail: buck353@okstate.edu

URL address

http://www.ansi.okstate.edu/software/

Title - Name

CROSS BREEDING SIMULATION

Highlights

From data entered by the user, this program generates profit or loss by industry segment for pure-breds, two-breed terminal, three-breed terminal, three-breed rotational and three breed special cross. It is capable of using up to 14 different breeds of cattle.

Contact

Burditt, Buchanan (Oklahoma State University)

URL address

http://www.clues.abdn.ac.uk:8080/directory/
Animal/Animal17.html

Title - Name

DESIRE – TARGET YOUR GENETIC GAINS

Highlights

This program is designed to help exploring the possible outcomes of a breeding program, in terms of predicted genetic gains for a number of traits. Setting desired gains restricts the possible range of genetic change for other traits. DESIRE is a dynamic tool to help you surf the n-dimensional (n-trait) space of possible outcomes from a simple breeding program.

Contact

Brian Kinghorn, Univ of New England, Armidale, Australia, Fax: +61 267 73 3275 and Sygen International, Franklin, USA, Fax: +1 270 586 4190. E-mail: bkinghor@une.edu.au (for details on contact,
see: http://www-personal.une.edu.au/~bkinghor/contact.htm)

URL address

http://www-personal.une.edu.au/~bkinghor/desire.htm

Title - Name

DFREML New Version (WOMBAT)

Title - Name

DISPAN

Highlights

DISPAN (Genetic Distance and Phylogenetic Analysis) is designed to

compute the following:

1. Average heterozygosity and its standard error for each population
2. Gene diversity (Ht) and its associate parameters, Hs, and Gst
3. Standard genetic distances (D) between populations
4. Standard errors of standard genetic distances
5. DA distances between populations

It also constructs phylogenetic trees (dendrograms) by using theneighbor-joining (NJ) method and the unweighted pair group-method with arithmetic mean (UPGMA) from matrices of either D or DA distances. Bootstrap tests for these trees can be performed.

Contact

URL address

http://www.bio.psu.edu/People/Faculty/Nei/Lab/
Programs.html

Title - Name

DISTANCE - PLOT GENETIC DISTANCES BETWEEN POPULATIONS

Highlights

Genetic distances between populations (or between individuals) are supplied. The program uses an evolutionary algorithm to find suitable placings on a 2-dimensional surface.

Contact

URL address

http://www-personal.une.edu.au/~bkinghor/distance.htm

Title - Name

FLUCTUATE

Highlights

FLUCTUATE estimates the effective population size and a exponential growth rate of a single growing population using non-recombining sequences. It fits the model, which has a single population, which has been growing (or shrinking) according to an exponential growth law. It estimates 4Nu and g, where N is the effective population size, u is the neutral mutation rate per site, and g is the growth rate of the population.

Contact

URL address

Title - Name

THE FREE SOFTWARE FOUNDATION

Highlights

The Free Software Foundation (FSF), is dedicated to promoting computer users' rights to use, study, copy, modify, and redistribute computer programs. The FSF promotes the development and use of free software, particularly the GNU operating system, used widely in its GNU/Linux variant.

URL address

www.fsf.org

Title - Name

GENSTAT DISCOVERY EDITION 2

Highlights

GenStat is a comprehensive statistics system which offers ease-of-use through a Windows menu interface, or power and flexibility for the more experienced user through a powerful command language interface. One of the main strengths of GenStat is the vast range of statistical techniques available which have been tested time and again by practicing statisticians, across many applications and disciplines.

Contact

URL address

Title - Name

GENUP: COMPUTER AIDED LEARNING FOR QUANTITATIVE GENETICS

Highlights

GENUP contains a number of learning modules. Each of these is designed to help you master concepts in Quantitative Genetics and its application to Animal Breeding. These modules are largely algorithm-based rather than information-based, meaning that you are given opportunities to play with the properties of the subject rather than be given information about the subject.

Contact

URL address

Title - Name

GETTING STARTED IN GIS – INTRODUCTORY EXERCISES

Highlights

Contact

ASSIST, Midlands Regional Research Laboratory, University of Leicester, Leicester, LE1 7RH

URL address

Title - Name

INBREEDING CALCULATOR

Highlights

Calculates the inbreeding of all individuals in a given pedigree that may be stored as a data file or entered directly into the portion of the program that calculates inbreeding.

Contact

Burditt, Buchanan (Oklahoma State University)

URL address

http://www.clues.abdn.ac.uk:8080/directory/Animal/
Animal26.html

Title - Name

LAMARC - LIKELIHOOD ANALYSIS WITH METROPOLIS ALGORITHM USING RANDOM COALESCENCE

Highlights

LAMARC is a package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations. It approximates the summation of likelihood over all possible gene genealogies that could explain the observed sample. The programs are memory-intensive but can run effectively on workstations or modern microcomputers. The package is continually expanding and more executables for different machines will become available soon.

Contact

URL address

http://evolution.genetics.washington.edu/lamarc.html

Title - Name

Microsoft Producer 2003

Highlights

Free software to licensed users of PowerPoint 2003 and Microsoft PowerPoint version 2002. Using MS Producer you can record either audio or video with audio and synchronize it with PowerPoint slides. This means that viewers from a computer can see and hear you, for example, at the same time as they see your PowerPoint slides. The only additional equipment needed to produce the presentation is a microphone, and, if desired, a video or web camera. MS Producer might be useful in distance education, or to give students the possibility to "re-visit" a lecture for rehearsal. For downloading the software and for examples of Producer presentations, see the website given below.

Contact

URL address

Title - Name

MIGRATE: ESTIMATION OF MIGRATION RATE AND EFFECTIVE POPULATION SIZE

Highlights

Migrate is part of Lamarc, a system for doing Likelihood Analysis with Metropolis Algorithm using Random Coalescence. It estimates the effective population sizes and migration rates of n constant population using non-recombining sequences, microsatellite data or enzyme electrophoretic data. It estimates effective population size and past migration rates between two or n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes.

Contact

URL address

Title - Name

MULTIPLE GENE POPULATION SIMULATION

Highlights

This program enables you to consider the arrangement of alleles along a genetic code (from 4 to 32 sites) and see how this code can be influenced by the “sorting” done by evolutionary forces during up to 500 generations. The first generation is a random arrangement of alleles that will be exposed to the evolutionary forces you select. Up to 10 different alleles are possible at each site along the code.

Contact

Oakleaf Systems, P.O.Box 472, Decorah, Iowa 52101, USA E-mail: oakleaf@mboxes.com

URL address

http://www.clues.abdn.ac.uk:8080/directory/Ecology/
Ecology32.html

Title - Name

OPEN OFFICE

Highlights

Open Office is a product that delivers the benefits of open-source software to mass-market users, delivering essential everyday software tools completely free of charge. It is translated into over 30 languages, and is available on all major computing platforms (Microsoft Windows, Mac OS X X11, GNU/Linux, Solaris). It is compatible with all other major office suites, and is free to download, use, and distribute.

URL address

www.openoffice.org

Title - Name

PEDIGREE HERD MANAGER

Highlights

With the ability to hold almost limitless records for up to 15 lactation’s per cow, the Pedigree Herd Manager provides a window onto your cows performance at any given time over any period. The added facilities for quota prediction, tracking and management make this program essential to any dairy farmer hoping to capitalize on the changes taking place in the milk industry. Over the years Datag has listened keenly to the opinions of both pedigree and commercial dairy farmers and has built this program up to contain many of the suggestions made. The software has been developed by a practical dairy farmer with much input from specialists to ensure that it covers every aspect of management.

Contact

Farm Computer Systems, Blackmoss Farm, Blackmoss Road, Dunham Massey, Altrincham Cheshire WA 14 5RG E-mail: enquiries@datag.co.uk

URL address

http://www.clues.abdn.ac.uk:8080

Title - Name

PEDIG: A FORTRAN PACKAGE FOR PEDIGREE ANALYSIS SUITED FOR LARGE POPULATIONS

Highlights

Software (in Fortran) specifically developed for analysis of large populations to calculate probabilities of gene origin, relastionship and inbreeding coefficient, and to calculate the quality of pedigree information.

Contact

Didier Boichard

URL address

http://dga.jouy.inra.fr/sgqa/diffusions/pedig/noticeE-C.htm

Title - Name

PEDIGREE VIEWER

Highlights

The program draws and manipulates pedigree diagrams. It reads your simple data file and displays the full pedigree structure on the screen. A large pedigree of thousands of animals can be displayed on the screen. Inbreeding coefficients and BLUP estimates of breeding value can be calculated and added to the list of displayable data. The program can be useful for navigating around a pedigreed data set to get a feel for its structure and any problems it might contain. Embryo transfer matings are usually easy to spot.

Contact

Brian Kinghorn, Univ of New England, Armidale, Australia, Fax: +61 267 73 3275 and Sygen International, Franklin, USA, Fax: +1 270 586 4190. E-mail: bkinghor@une.edu.au (for details on contact, see: http://www-personal.une.edu.au/~bkinghor/contact.htm)

URL address

http://www-personal.une.edu.au/~bkinghor/
pedigree.htm

Title - Name

PEST

Highlights

PEST is a user friendly Fortran program for prediction of breeding values in practical animal breeding. It covers fixed, random and mixed models. A parameter file consists of input data description, the statistical model, output, data transformations etc.

Some further features of PEST are: Treatment of missing values; Different incidence matrices for some or all traits; Inclusion of relationship among animals; Treatment of inbreeding; Genetic group models; Heterogeneous variances; Treatment of animal, sire, sire dam models; Prediction error variances for BLUPs and standard errors of BLUEs.

Contact

Eidert Groeneveld, Federal Agricultural Research Centre (FAL), Institute for Animal Breeding, 31535 NEUSTADT-MARIENSEE, Germany, FAX: +49 (0)5034 / 871 143. E-mail: Eildert.Groeneveld@fal.de

URL address

http://www.tzv.fal.de/~eg/

Title - Name

PHYLOGENETICS SOFTWARE RESOURCES

Highlights

Links to phylogenetics software lists and computer programs

Contact

Museum of Paleontology, Univ of California, Berkeley

URL address

http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html

Title - Name

PIGPRO

Highlights

Pig breeding (individual sows and boars), feeding and financial – practical pig farming version. Outdoor option; Health & Medication and Movement records to UK regs. There are many other programs available form HM Boot on pig farming and management.

Contact

H.M. Boot, Bleak House Farm, Aston, Nantwich, Cheshire CW5 8DS

URL address

http://www.clues.abdn.ac.uk:8080/directory/Animal/
Animal33.html

Title - Name

POPULATION GENETICS SIMULATION PC

Highlights

This is a graphical simulation of the effects of mutation both forwards and reverse, natural selection (8 types), gene flow (emigration and immigration), genetic drift (up to 500 individuals) on the rate at which gene frequencies change within a population. Allele frequency plots are displayed as the program can simulate up to 1000 generations. Users can mimic any 2-allele system, with graphical plots, or the complete listing of allele frequencies can be printed. Over 20 sample simulation problems (with solutions) are included that can be copied and used as student worksheets.

Contact

Oakleaf Systems, P.O.Box 472, Decorah, Iowa 52101, USA E-mail: oakleaf@mboxes.com

URL address

http://www.clues.abdn.ac.uk:8080/directory/Ecology/
Ecology33.html

Title - Name

QTL CARTOGRAPHER

Highlights

QTLCART is an interactive program for mapping quantitative trait loci (QTLs). Models are based on 1) linear regression 2) interval mapping 3) composite interval mapping. Currently it can analyse F2 and Backcross progeny. One must have genetic linkage map prepared before looking for QTLs. QTLCART can use output from MAPMAKER. It can work with simulated or real data. It provides the option of simulating data within QTLCART.

Contact

Chris Basten (basten@esssjp.stat.ncsu.edu )

Title - Name

QTL EXPRESS

Highlights

The purpose of QTL Express is to provide user-friendly software for the analysis of quantitative trait data from outbred populations. The focus is on simple, but robust and powerful analytical tools. Therefore, regression, least squares and variance component methods of analysis will be implemented. At present, regression analyses of data from an F2 population derived from a cross between two outbred populations and regression analysis of data from half-sib families have been implemented.

Contact

George Seaton (George.Seaton@ed.ac.uk )

URL address

Title - Name

QUANTITATIVE GENETICS RESOURCES

Highlights

Links to software in Genetics, Animal Breeding and Statistics

Contact

M. Lynch, Univ at Bloomington and B. Walsh, Univ of Arizona E-mail: jbwalsh@u.arizona.edu

URL address

http://nitro.biosci.arizona.edu/zbook/book.html#Links

Title - Name

R (THE R PROJECT FOR STATISTICAL COMPUTING)

Highlights

R is `GNU S', a freely available language and environment (software) for statistical computing and graphics. It provides a wide variety of statistical and graphical techniques: linear and non-linear modelling, statistical tests, mixed models and variance components, time series analysis, classification, clustering, etc. R can be extended via packages. There are about eight packages supplied with the R distribution and many more are available through the CRAN family of Internet sites covering a very wide range of modern statistics.

R can be downloaded free of charge and can continuously be up-dated. Manuals are included as pdf files.

URL address

http://www.R-project.org/
http://cran.r-project.org/

Title - Name

RECOMBINE 

Highlights

RECOMBINE estimates the effective population size and per-site recombination rate of a single constant-size population. It fits a model, which has a single population of constant size with a single recombination rate across all sites. It can accommodate either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism) data. It estimates 4Nu and r, where N is the effective population size, u is the neutral mutation rate per site, and r is the ratio of the per-site recombination rate to the per-site mutation rate.

Contact

Mary K. Kuhner, Jon Yamato, Department of Genetics, University of Washington, Box 357360, Seattle, WA 98195-7360, USA

E-mail: mkkuhner@genetics.washington.edu

URL address

http://evolution.genetics.washington.edu/lamarc/
recombine.html

Title - Name

SELACTION

Highlights

SELACTION is a computer program that predicts response to selection and rates of inbreeding for practical livestock improvement programs. The program uses deterministic simulation and requires little computing time; it can be used as an interactive optimization tool. The use of SelAction requires a license. There are two types of licenses; a license for commercial purposes and a license for non-commercial purposes. A license for non-commercial purposes can be obtained by paying an administration fee of EURO 150, to cover the cost of setting up a license agreement.

Contact

Dr.Ir. P. Bijma (piter.bijma@alg.vf.wau.nl ) Animal Breeding and Genetics Group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700 AH Wageningen The Netherlands, tel +31 317 482731/482335, fax +31 317 483929

URL address

http://www.zod.wau.nl/abg/

Title - Name

STUDY SKILLS – GUIDANCE PROGRAM FOR STUDENTS

Highlights

Study Skills 1.1 is a computer-based learning program addressing students. Advice is given (in bullet form) on e.g. the following aspects: Lectures, seminars, tutorials, note taking, efficient reading, examination, writing essays, presentations, etc. A free, brief demo version can be downloaded. The complete program is purchased.

Contact

Clifton Press, P O Box 100, Manchester, M20 6GZ Tel: 0161 432 5811, Fax: 0161 443 2766

E-mail: info@mantex.demon.co.uk

URL address

http://www.mantex.co.uk/software/study.htm

Title - Name

SURVIVAL OF THE FITTEST – POPULATION GENETICS

Highlights

Teaches the principles of population genetics. Allows the student to ‘breed’ their own animals and select which animals they wish to continue to breed in the next generation. Includes manuals.

Contact

Software Production Associates Ltd, P O Box 59, Tewkesbury, Gloucestershire, GL20 6AB

URL address

http://www.clues.abdn.ac.uk:8080/directory/
Ecology/Ecology36.html

Title - Name

VCE

Highlights

VCE is a program to estimate covariance matrices in a rather general manner. Three methods are available: 1) REML using analytical gradients, 2) a Monte-Carlo EM which also does REML and 3) Gibbs sampling. VCE is completely rewritten in Fortran90. It comes as executables ready to run and has very flexible model definitions.

Contact

Eidert Groeneveld, Federal Agricultural Research Centre (FAL), Institute for Animal Breeding, 31535 NEUSTADT-MARIENSEE, Germany, FAX: +49 (0)5034 / 871 143. E-mail: Eildert.Groeneveld@fal.de

URL address

http://www.tzv.fal.de/~eg/

Title - Name

WOMBAT

Highlights

WOMBAT replaces DFREML. WOMBAT is aimed at the analysis of data from animal breeding programmes. It accommodates most models commonly fitted for such data, and employs up-to-date methods for ordering the mixed model equations and maximising the likelihood. It is particularly suitable for analyses of large data sets fitting simple models. WOMBAT performs uni- and multivariate analyses for both standard and random regression models. For the latter, a choice of bases is available, including polynomial and B-spline functions. There are no license requirements, but it is a condition that a) use of WOMBAT is credited in any publications or reports, and b) that WOMBAT is not used commercially. Released in August 2006

Contact

K. Meyer ( kmeyer@pobox.une.edu.au)

URL address

Title - Name

XLSTAT

Highlights

XLSTAT offers different functions to enhance the analytical capabilities of MS Excel. Runs on all Excel versions from version 97. XLSTAT includes functionalities for preparing and describing data, analyzing data (e.g. principal component analysis, discriminant analysis, clustering), modeling (e.g. regression, ANOVA, parametric and non-parametric tests). Free trial version.

Contact

URL address