About GenAlEx 6.

Release History
GenAlEx 6.41 was released on Dec 20, 2010 to provide a bug fix for the Process Sequences option that appeared in GenAlEx 6.4. This release also improves compatibility for Intel Mac users running GenAlEx in the newly released Excel 2011. This version is strongly recommended as the replacement for all previous versions of GenAlEx. GenAlEx 6.4 was released on Aug 26, 2010. Version 6.4 fixed a number of minor bugs, provided full compatibility with Excel 2003, 2007 and 2010 on the PC, improved performance in Excel 2007/2010 on the PC, and also offered several new features described below.

What is new in GenAlEx 6.4?

One size fits all
From GenAlEx 6.4 onwards only a single version of GenAlEx will be distributed which can be run in Excel 2003 through to Excel 2010 on the PC, and on Excel 2004 and Excel 2011 on the Macintosh (Mac users please see below for more details). GenAlEx 6.4 now automatically assesses whether the current worksheet has 256 columns (*.xls) or 16,384 columns (*.xlsx), allowing you to seamlessly use both *.xls and *.xlsx files from within Excel 2007/2010/2011, or to use the same version of GenAlEx in both Excel 2003/2004, or Excel 2007/2010 (but not simultaneously, unless using different copies).

Improvements in Excel 2007 onwards

While GenAlEx 6.1 onwards has been broadly compatible with Microsoft Excel 2007, GenAlEx 6.4 has been optimized for Excel 2007/2010 with improvements in the memory management of variables that should enable users to run even larger data sets than previously. Furthermore, when running GenAlEx in Excel 2007, users may have noticed that it runs slower than in Excel 2003. One source of the problem is an Excel 2007 bug that is associated with the status bar that GenAlEx uses regularly to report to users the stage of calculations. This is particularly important information when running permutational tests for large data sets. If you notice the status bar blinking rapidly during a run, this will almost certainly indicate that the drawing of the status bar is slowing down GenAlEx calculations. GenAlEx 6.4 now reduces the number of calls to the status bar to minimise this problem. Extensive testing has confirmed equivalent speeds between Excel 2003 and Excel 2007 can now be obtained. Excel 2010 appears to offer overall performance improvements and increased options for customizing the software and is strongly recommended over Excel 2007. Although not found to be necessary on the PCs tested, a further option to turn of the status bar counter altogether is now provided. Use may wish to trial this option if their status bar continues to blink rapidly during runs.

Tip: Excel 2007 is widely reported to be slower than Excel 2003. This is in part due to the much larger size of the spreadsheet. Microsoft has addressed many of these issues in Excel 2010 and it is recommended that GenAlEx users either use Excel 2003 or Excel 2010. Meanwhile, check out sites such as the following for ways to improve performance of Excel more generally: http://msdn.microsoft.com/en-us/library/aa730921(office.12).aspx

Spatial analysis and Pops Means analysis bugs fixed

A bug in the reporting of the probability values P(r-rand<=r-data) for all Spatial analysis and Pops Mean analysis has been fixed. This bug affected the one-tailed tests for negative values only. Special thanks to Kris Hundertmark (Alaska, USA) for finding and reporting this problem.

Shannon analysis changes

Improvements in the listing of the formulae at the end of each Shannon analysis have been made to avoid ambiguity and improve readability. Mean values for the exponential statistics (e.g. sHua2) are now calculated as the exponential of their respective mean values. While the mean Nm is calculated form the mean sHua avoiding problems when some loci have sHua = 0 (which gives Nm = #DIV/0!). A new option that allows uses to set the threshold at which a small sHua value should be treated as if zero is also provided (default = 0.0001). This option should be used cautiously, but may
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be useful to avoid spurious mean values when the data set includes a locus with limited variation. Of course any locus that is monomorphic across all samples should be removed from the Shannon analysis to avoid Nm = #DIV/0! for that locus. Special thanks to Bill Sherwin (NSW, Australia) and Eric Karlin (New Jersey, USA) for discussions that lead to these improvements.

New Merge Cols option

A powerful new Merge Cols option under Raw Data allows you to merge two data sets that have a common unique numerical identifier for each sample. For example, in the case illustrated below Haploid Subset 1 with 4 data columns (4 loci in this case) is merged with Haploid Subset 2 containing 10 columns (including non-genetic data) to give the final combined data set. Note that Cell A1 normally reserved for No. of Loci in the GenAlEx format is used in this case for the No. of Cols. Haploid Subset 1 in Worksheet 1

Haploid Subset 2 in Worksheet 2

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The Merged Columns Output in Worksheet 3

Export to Network
GenAlEx 6.4 now offers export of haploid data such as cpSSRs or Y-chromosome SSRs to the free Phylogenetic Network software by Fluxus Engineering: http://www.fluxus-engineering.com/sharenet.htm

Other new options

A range of other minor changes have also been made in this version including: Graph->XY from Range that allows you to quickly plot an XY graph from a range. Parameters->Count List from Range that offers a convenient way to assemble a count of items in a list. Parameters->Row and Column that returns the row and column number of a cell which can be useful when using the various Raw Data merge options. There have also been a number of improvements in operation and labeling of the outputs generated under the Stats menu options.

Installation of GenAlEx 6.4

The procedure for installing GenAlEx 6.4 and 6.41 is the same as for previous versions of GenAlEx. GenAlEx is provided as an Excel Add-in, a compiled module and its associated GenAlEx menu. Your downloaded file may initially be in the zipped format. Use the extract option to unzip the download and save the files to a dedicated folder of your choice. You can work with GenAlEx directly from this folder. Separate instructions for Excel Pre-2007 on PC, Excel 2007/2010 on PC and Excel 2011 for Intel Mac are provided below. Notes for Macintosh Users On Macintosh computers, GenAlEx can be run in Excel 2004 and Excel 2011, but not Excel 2008. This is because Microsoft removed the ability of Excel 2008 to run Visual Basic for Applications (VBA), the macro language of Microsoft Office. Note that Excel 2011 has been released early (Oct 2010), but can only be run on an Intel-based Macs. Therefore, if you are running a PPC Macintosh you can only run GenAlEx in Excel 2004, or earlier.

Loading GenAlEx in Excel Pre-2007 on PC

Step 1. Step 2. Copy the GenAlEx Add-in (e.g. GenAlEx 6.4.xla) to your choice of location on your computer. This should preferably be in a dedicated folder. Launch MS Excel. Choose Open from the File menu, locate the GenAlEx Add-in, then click the OK button.

Tip: Alternatively, you can launch GenAlEx and Excel simultaneously by clicking directly on the GenAlEx Add-in file.
Step 3. Depending on the settings of your Excel program, Excel may warn you that GenAlEx contains macros. Click the Enable button to proceed.
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Step 4.

In a few seconds the GenAlEx splash screen will appear, click to hide, the GenAlEx menu will appear in the Excel menu bar, just before the Help menu.

Step 5.

If you do not see the security warning dialog box and/or GenAlEx does not launch, you may see the message below instead. In this case, continue to step 6.

Step 6.

From the Excel menu Tools, choose Options. At the options dialog box click the Macro Security button on the Security tab. In the next dialog box, choose Medium for the security level. Now return to step 1 to launch GenAlEx.

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Optimizing Font Size for GenAlEx in Excel Pre-2007 PC

GenAlEx output is optimized for a font size of 10 pt. If not already, you should therefore set the Excel default font size to this setting. Note that this setting does not over ride the font settings embedded in existing worksheets. To ensure GenAlEx output is in 10 pt, you may wish to copy data (or data sheets) to new workbook that has been created after the Excel default font is set to 10 pt as outlined below.
Step 1. Step 2. From the Excel menu Tools, choose Options. At the options dialog box click the General tab. Set the standard font size to 10 pt.

Loading GenAlEx in Excel 2007 or Excel 2010 on PC

Step 1. Step 2. Launch Excel 2007 or Excel 2010. In Excel 2007, open the GenAlEx Add-in (e.g. GenAlEx 6.4.xla) via the Microsoft Office Button (top left of screen). In Excel 2010, open the GenAlEx Add-in via the File menu. When prompted, by the Security Notice, choose Enable Macros.

Step 3.

Step 4.

Shortly the GenAlEx splash screen will appear.

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Step 5.

Click the Add-Ins tab to show the Add-Ins ribbon. The GenAlEx menu will appear on the right, along with any other installed Add-Ins you may be running. When using GenAlEx you may find it convenient to turn off Minimize Ribbon so that the GenAlEx menu is always accessible when the Add-Ins ribbon is shown. You can access this option by right-clicking the ribbon.

Optimizing Font Size for GenAlEx in Excel 2007 on PC

GenAlEx output is optimized for a font size of 10 pt. If not already, you should therefore set the Excel default font size to this setting. Note that this setting does not over ride the font settings embedded in existing worksheets. To ensure GenAlEx output is in 10 pt, you may wish to copy data (or data sheets) to new workbook that has been created after the Excel default font is set to 10 pt as outlined below.
Step 1. Step 2. Click the Microsoft Office button (top left of screen), then Excel Options. Set the default Font Size for new workbooks to 10 pt under the option When creating new workbooks.

Optimizing Font Size for GenAlEx in Excel 2010

GenAlEx output is optimized for a font size of 10 pt. If not already, you should therefore set the Excel default font size to this setting. Note that this setting does not over ride the font settings embedded in existing worksheets. To ensure GenAlEx output is in 10 pt, you may wish to copy data (or data sheets) to new workbook that has been created after the Excel default font is set to 10 pt as outlined below.
Step 1. Step 2. Step 3. Click the File menu, then click Options. From the Excel Options dialog choose General. Set the default Font Size for new workbooks to 10 pt under the option When creating new workbooks.
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Loading GenAlEx in Excel 2011 on Intel Mac

Step 1. Step 2. Step 3. Launch Excel 2011. From within Excel, open the GenAlEx Add-in (e.g. GenAlEx 6.41.xla) via the File menu. When prompted, by the Security Notice, choose Enable Macros.

Step 4.

Shortly the GenAlEx splash screen will appear.

Step 5.

Now you can access GenAlEx options from the GenAlEx menu.

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Optimizing Font Size for GenAlEx in Excel 2011 on Intel Mac

GenAlEx output is optimized for a font size of 10 pt on both PC and Mac. If not already, you should therefore set the Excel default font size to this setting. Note that this setting does not over ride the font settings embedded in existing worksheets. To ensure GenAlEx output is in 10 pt, you may wish to copy data (or data sheets) to new workbook that has been created after the Excel default font is set to 10 pt as outlined below.
Step 1. Step 2. Step 3. Step 4. Click the Excel menu, then click Preferences. From the Excel Preferences dialog choose General. Set the default Font Size for new workbooks to 10 pt under the option Standard font. Excel will warn that you must restart Excel for this option to take effect.

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Learning More About GenAlEx

Extensive documentation about GenAlEx is freely available from The Australian National University, Canberra, Australia. http://www.anu.edu.au/BoZo/GenAlEx/. A good place to start learning about GenAlEx is to access the self-paced tutorial modules that we have provided on population genetic analysis. These tutorials are based on material we have prepared to support our various graduate workshops and provide step-by-step instructions for using GenAlEx to perform a wide range of population genetic analysis. A Quick Start guide that includes some introductory exercises is also distributed with the GenAlEx Add-in, but should not be seen as a substitute for completing these tutorials. The GenAlEx Appendix 1 document is also an invaluable source of information. This 30 page document summarizes the methods and statistics available in GenAlEx, along with more than 70 supporting references. The new updated version of Appendix 1 for GenAlEx 6.4 also includes cross referencing to the Tutorials.

GenAlEx Tutorials An Overview of Topics

Part 1 - An Introduction to Frequency-Based Population Genetic Analysis Topics include: scoring genetic markers, Allele Frequency, Heterozygosity, F-statistics, Nei Genetic Distance, Shannon Diversity Indices and Hardy-Weinberg Equilibrium. Part 2 - Genetic Distance and Analysis of Molecular Variance (AMOVA) Topics include: Haploid, Codominant and Binary Genetic Distance, AMOVA and F-statistics. Part 3 - Spatial Genetic Analysis Topics include: Principal Coordinate Analysis (PCA), Mantel Tests for Matrix Correspondence and Spatial Autocorrelation Analysis. Part 4 - Advanced Frequency-Based Analysis Topics include: DNA Profile Probability, Probability of Identity, Probability of Exclusion, Population Assignment and Pairwise Relatedness. Part 5 - Advanced Features Including Data Import and Export Topics include: Working with DNA sequences, importing and processing raw genotypic data, and exporting data from GenAlEx to other software packages. The Stats menu and how to customise the GenAlEx menu are also covered briefly. Part 6 - TwoGener Topics include: Male gametic inference, male gametic distances, gametic AMOVA.

Other GenAlEx documentation

In addition to the tutorial modules and the updated Appendix 1, the comprehensive guide to GenAlEx 6, although partially outdated, nonetheless remain useful for most operations. This guide is available in both English and Spanish. A new version of the guide is planned for the forthcoming release of GenAlEx 6.5 An overview of GenAlEx 6 features is also provided in: 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. Note this official reference refers to the software package in lower caps: GENALEX 6. Please use this text format for publication purposes. If you are unable to obtain a copy of this program note, reprints are freely available on request (email: rod.peakall@anu.edu.au).
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