GenAlEx (Genetic Analysis in Excel) is a user-friendly software add-in for teaching and research in population genetics. It enables powerful data analysis and visualization within Microsoft Excel, supporting genetic diversity, structure, and distance metrics.

Content navigation

Overview

Genetic Analysis in Excel

GenAlEx offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers. When combined with its user-friendly interface, rich graphical outputs for data exploration and publication, tools for data manipulation and export options to many other software packages, we believe that GenAlEx offers an ideal launching pad for population genetic analysis by students, teachers and researchers alike.

Import and export options

Import export options

GenAlEx offers data import from several popular formats and tools for importing and manipulating raw data from DNA sequencers. Export to more than 30 other data formats is provided, enabling access to myriad other software packages. For example, direct export is offered to such programs as GENEPOP (Rousset 2008) and STRUCTURE (Pritchard et al. 2000), and via these same formats to many other programs, including genetic packages in R such as adegenet (Jombart 2008) and pegas (Paradis 2010).

Releases

If you are not already a registered user of GenAlEx, we strongly recommend that you register before downloading GenAlEx 6.5.  Registered user are notified of major GenAlEx updates only.  Typically you will receive only 1 or 2 email contacts a year.  We do not use the email address you provide for any other purpose. 

GenAlEx 6.51b2 - Released June 2018

In this beta release of GenAlEx 6.51 we offer the new QDiver analysis option introduced in our publication

GenAlEx 6.51b2.xlam is fully compatible with Excel 2016 on Windows (32-bit & 64-bit), and is expected to be backwards compatible to Excel 2010. Note that this version of GenAlEx is not yet fully compatible with Excel 2016 (64-bit) on the Macintosh. Nonetheless, our recent tests in March 2018 show that most GenAlEx options do run successfully, but with some minor Dialog box and Ribbon button image issues.  These minor, mostly cosmetic issues, have yet to be fully resolved.

GenAlEx 6.503 - Released Dec 2016

This release for Excel 2016 running in Windows offered new access to all GenAlEx options via the Excel Ribbon, while at the same time remaining backwards compatible to Excel 2010. Prior to this release, all access to GenAlEx options was via the GenAlEx menu.  The location of the GenAlEx menu has depended on the version of Excel used, and the operating system. The Excel Ribbon now provides a common interface and access point to GenAlEx options across Excel versions and operating systems.

Image
GenAlEx Excel integration

Recent tests indicate Visual Basic for Applications (VBA) functionality on the Macintosh is increasingly being improved by Microsoft.  Consequently, most GenAlEx options can now be run in GenAlEx 2016 on the Macintosh via the Ribbon, although some minor Dialog box and Ribbon button image issues remain.  These minor, mostly cosmetic issues, have yet to be fully resolved.  We apologize to our long-standing GenAlEx users on the Macintosh for these issues which are beyond our control.

GenAlEx 6.503.xlam is fully compatible with Excel 2016 on Windows, and is expected to be backwards compatible to Excel 2010. Note that this version of GenAlEx is not yet fully compatible with Excel 2016 on the Macintosh. Nonetheless, our recent tests in March 2018 show that most GenAlEx options do run successfully, but with some minor Dialog box and Ribbon button image issues.  These minor, mostly cosmetic issues, have yet to be fully resolved.

GenAlEx 6.5 - Released in September 2015

GenAlEx 6.502.xla is fully compatible with Excel 2003 to Excel 2016 on Windows.  On Mac it is compatible with Excel 2004 and 2011.

GenAlEx 6.502 offered new Shannon Diversity Analysis options as described in: Smouse, P.E., Whitehead, M.R., and Peakall, R. (2015) An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation. Molecular Ecology Resources 15, 1375-1384 (DOI 10.111/1755-0998.12422)

GenAlEx 6.5 - Released in 2012

Genetic Analysis in Excel is a popular cross platform package for population genetic analysis that runs within Microsoft Excel. GenAlEx offers analysis of codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. In GenAlEx 6.5 we introduce exciting new features including calculation of new estimators of population structure: G’ST, G’’ST, Jost’s Dest, and F’ST via AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data, and heterogeneity tests for spatial autocorrelation analysis. Direct data export is provided to more than 30 other software packages, and indirectly via common formats to many more packages. New teaching tutorials and extra step-by-step options are also included. The comprehensive independently written guide has been fully revised.

Guide

Tutorials

We are pleased to offer a series of self-paced tutorials on population genetic analysis that employ hand calculations and exercises within GenAlEx. These are drawn in part from the graduate workshops that we have offered (jointly and independently), around the world.  Click the links below to download any tutorials of interest. In 2012, Tutorials 1-6 were revised to bring them up to date with the new features of GenAlEx 6.5. The newer Trouble Shooting Tutorial is strongly recommended for all users.  It provides helpful tips for solving some of the issues that may prevent some data sets from running.

An Introduction to Frequency-Based Population Genetic Analysis

Scoring genetic markers, Allele Frequency, Heterozygosity, F-statistics, Nei Genetic Distance, Shannon Diversity Indices and Chi-square tests for Hardy-Weinberg Equilibrium

Genetic Distance and AMOVA

Haploid, Codominant and Binary Genetic Distance, AMOVA and F-statistics

Spatial Genetic Analysis

Principal Coordinate Analysis (PCoA), Mantel Tests for Matrix Correspondence and Spatial Autocorrelation Analysis

Advanced Frequency-Based Analysis

DNA Profile Probability, Probability of Identity, Probability of Exclusion, Population Assignment and Pairwise Relatedness

Advanced Features Including Data Import and Export

Working with DNA sequences, importing and processing raw genotypic data, exporting data from GenAlEx to other software. The Stats menu and how to customise the GenAlEx menu are also covered briefly.

TwoGener

Male gametic inference, male gametic distances, gametic AMOVA

Hierarchical Shannon Diversity Analysis

Troubleshooting

This tutorial provides helpful tips for troubleshooting when GenAlEx is initially unable to run some data sets.

Publications

  • Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539. Freely available: http://bioinformatics.oxfordjournals.org/content/28/19/2537
  • Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295.

Citation

From July 2012, GenAlEx has a dual citation (Peakall and Smouse 2006, 2012).  Please use this dual citation whenever you reference GenAlEx.  Note also that this dual citation applies for anyone using GenAlEx 6.1 onwards.  This is because the new application note by Peakall and Smouse (2012) is an update that covers the features in GenAlEx that have been progressively released since the original computer note of Peakall and Smouse (2006). 

That is, Peakall and Smouse (2012) is not a substitute for Peakall and Smouse (2006), but rather an update to be read and cited with the original reference. Wherever possible, we would be grateful if you could update your citation and references in any existing manuscripts.

  • Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539. Freely available as an Open access article from here: http://bioinformatics.oxfordjournals.org/content/28/19/2537
  • Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes. 6, 288-295. Abstract available here

Authors

Professor Rod Peakall

Rod Peakall

Ecology and Evolution
Research School of Biology
The Australian National University
Acton ACT 2601 Australia
rod.peakall@anu.edu.

Rod Peakall is a Professor in Evolutionary Biology. His research has long employed multidisciplinary approaches spanning the fields of ecology, genetics, molecular biology and chemical ecology for investigating a range of pure and applied questions in pollination biology, chemical ecology, evolutionary biology and conservation biology. His integration of multidisciplinary tools allows novel insights that are not possible on their own.

Presently his research fall into two main themes. The first theme concerns the evolution of specialized pollinator interactions and the role of pollinators in plant speciation, with Australian orchids and their pollinators the prime focus. The second theme concerns the analysis of population genetic structure and its implications for dispersal, mating systems, conservation and evolution. The target species for this research include bacteria, fungi, plants, birds, small mammals and whales.

Professor Peter Smouse

Peter Smouse

Department of Ecology, Evolution and Natural Resources
School of Environmental and Biological Sciences
New Brunswick NJ 08901-8551 USA

Peter Smouse is a Professor in Theoretical & Applied Genetics. As a theoretical and statistical population geneticist, he has worked on both theoretical and empirical aspects of population genetic analysis in a wide variety of organisms, including forest trees, agronomic crops, bacteria, marine and freshwater fish, insects, and humans.

Disclaimer

This program is provided free of charge by the authors. While every effort has been taken to ensure the accuracy of the results and the smooth operation of the program, we regret that we are unable to take responsibility for unintentional errors or problems that may be encountered by users. We are also unable to provide individualized support for users of the program.  If you are a new user, please refer to the extensive documentation we provide including the Guide to GenAlEx and the supporting tutorials, both of which offer step-by-step instructions.