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Welcome to GenAlEx 6.1! GenAlEx 6.1 is an essential upgrade that replaces GenAlEx 6.

In addition to minor improvements in the interface and the usual bug fixes, GenAlEx 6.1 offers some exciting new features for both teachers and researchers. For teachers, some of the new features include: more step-by-step output options, more tools for data exploration, and new tools for teaching topics such as permutation and bootstrapping. For researchers, we have considerably expanded the Analysis of Molecular Variance options to include more detailed F-statistics analysis, additional analysis outputs by locus, additional specialized permute options, additional graphing options, and the output of Linearized Fst. We have also added support for Binary Haploid data, expanded the range of TwoGener options and added Nei Unbiased Heterozygosity and Nei Unbiased Genetic Distance estimates for all types of data. GenAlEx 6.1 is fully compatible with Excel 2007. This includes the ability to take advantage of the substantially increased number of columns from 256 pre-Excel 2007 to 16,384 columns in Excel 2007. This capability will be particularly welcomed by AFLP users, whose binary data sets frequently exceed more than 256 polymorphic loci. The extra columns per worksheet will also allow expanded capability for working with DNA sequences within GenAlEx. If you intend to use GenAlEx 6.1 in Excel 2007, be sure to read the additional information provided below. GenAlEx 6.1 now provides direct export of data to more than 20 other genetic software packages or formats including: AFLP-SURV, Alleles in Space, Arlequin, Cervus, FAMD, Famoz, Fdist2, GDA, GeneClass, GenePop, GeneticStudio, Kingroup, MEGA, MSA, MsVAr, Nexus, Phylip. POLDISP, PopGene, SPAeDI, Structure and TFPGA packages. In addition, indirect export to other packages such as Fstat and BAPS is available via the GenePop export format. GenAlEx 6.1 Documentation Presently specific documentation on the new features in GenAlEx 6.1 is limited to an updated Appendix 1 that includes formulas and references for the new procedures offered. A forthcoming Appendix 6 on TwoGener analysis is planned for early in 2008. The current Guide to GenAlEx 6 by Nicola Flanagan (available in both English and Spanish) has not yet been updated to reflect the additional features in GenAlEx 6.1. For now, we hope that in combination with the GenAlEx 6 guide that GenAlEx users will find most of the new features in GenAlEx 6.1 self-explanatory. Thank you for using GenAlEx 6.1. Enjoy! Rod Peakall and Peter Smouse Dec 2007

Read Me File GenAlEx 6.1

Important information about using GenAlEx 6.1 in Excel 2007 Given the radical new user interface of Excel 2007, users may find it hard to locate the GenAlEx menu. As with pre Excel 2007 Add-Ins generally, Add-ins are now accessed from a menu on the Add-Ins ribbon. The following instructions should assist first time users of GenAlEx 6.1 to access GenAlEx features within Excel 2007. Steps for Loading GenAlEx 6.1 in Excel 2007 1. Launch Excel 2007. 2. Open GenAlEx 6.1.xla via the Microsoft Office Button (top left of screen). 3. When prompted, by the Security Notice, choose Enable Macros.

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Shortly the GenAlEx 6.1 splash screen will appear.

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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 show. You can access this option by right-clicking the ribbon.

Read Me File GenAlEx 6.1

Note that in future releases of GenAlEx we hope to be able to customise the location of the GenAlEx menu for easier access. For now we are stuck with the default options provided by Excel 2007.

Read Me File GenAlEx 6.1

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While less convenient (it takes an extra click to get to the GenAlEx menu) you can also access GenAlEx via the Quick Access Toolbar. To enable this option you will need to customise the Quick Access Toolbar by adding the Command Menu option. This command menu bar allows access to all commands shown on the Add-Ins Tab.

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As in earlier versions, GenAlEx 6.1 output is optimised for a Font Size of 10 pt. If not already set to this default. 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.

Read Me File GenAlEx 6.1

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To enable GenAlEx to take full advantage of the additional columns in Excel 2007, there is one more step. Go to GenAlEx->Options->Generic and click the option Full 2007 Compatibility, then choose Save. Should you subsequently open GenAlEx in an earlier version of Excel, the compatibility option will be re-set to Pre-2007 Compatibility. If you plan to work with both Excel 2007 and earlier versions of Excel you may wish to make a copy of GenAlEx specifically for Excel 2007, and save that copy with the Full 2007 Compatibility option. Be sure you are aware of the backward compatibility issues that using Excel 2007 can create if working with different versions of Excel.

Read Me File GenAlEx 6.1