ReadMe for NeEstimator Version 2.1 Major Update December 2017

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About the Major Update of v2.1 December 2017

Version 2.1 is a major update on V2.01. The changes largely enhance the linkage disequilibrium (LD) capacity of the software for the estimation of genetic effective population size. Enhancements include faster estimation of Burrows r, option to estimate r between loci on different chromosomes or linkage groups (user needs to upload linkage information), improved method of estimating jackknifed confidence intervals and improvements to handling low frequency alleles.

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You have downloaded the following files as a .zip package.


1)  NeEstimator2x1.jar (the graphical user interface or GUI)

2)  Ne2-1.exe (executable for Windows), Ne2-1M (executable for mac) and Ne2-1L (executable for Linux). For Mac and PC users, the GUI will automatically launch the correct version for your operating system. Linux users need to read the text below to start the software.

3)  A folder of test input files containing microsatellite and SNP-like data in several formats (e.g. 8Ne50.dat, 8Ne50.gen and Input_test_A.txt)

4)  A folder containing an example of a basic output file (eg. 8Ne50Ne.txt)

5)  A help folder containing the help file as a .pdf. The help file will launch on command from within the GUI using the pull-down menu.

6)  Accessory files outlining the mathematical details of methods implemented by the software.

7)  A folder of files for batch processing.

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To run the software :-

1. Unpack (expand) the zip package.

2. Place all files into a single folder (directory) on your hard drive.

3. Run the NeEstimator V2.1 software by starting the graphical user interface as follows:

   * Windows or Mac Users: Double click on the NeEstimator2x1.jar program. Mac users may receive a message "Can't be opened because it is from an unidentified developer". Hold down the control key and click the icon. Select the appropriate software (if prompted) and choose open.

   * Linux Users: From the command line execute:  "java -jar ./NeEstimator2x1.jar". 

4. Load an input file using buttons on the interface. 

5. Click "Run NeEstimator".

6. On completion, look for output in the same directory as the input file. 

7. Click the "?" and "info" buttons within the user interface for details regarding numerous other options.

8. Read the help file for further information.

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NeEstimator development team

December 2017

