UNSUPPORTED SOFTWARE: USE AT OWN RISK

Individual to Individual Genetic Distance Calculator

This program computes a genetic distance between all pairs of individuals. The shared allele distance is defined as one minus half the average number of shared alleles per locus.

New - avoiding the clipboard with local load/save

The Virtual Clipboard for large datasets

A note on multi-page input windows

(Click here to go to the population-level genetic distance calculator instead.)


As a quick check, the distances computed for the sample should be 1 minus the fraction of allele-copies present in both the individuals being compared. For example, the first two individuals below share 6 of their 10 allele copies, so the computed distance is
1 - 6 / 10 = 0.4 (notice that one allele is missing in each individual)
Click "Calculate!" to run this example, or "Clear Inputs" to enter your own data.
This program requires a Java-enabled browser. Perhaps your browser has Java disabled?

How to Read/Write Files on Your Machine

The virtual clipboard was a clunky work around for the security that Java-enabled browsers impose (with good reason!) on web-programs. Provided you trust that you are getting an unmodified copy of this program from our website, you can save a copy on your machine so that data can be read from or written to files directly on your machine, without going through the network and virtual clipboard. This procedure only works for Netscape browsers.

Here's how:

The VC buttons should be replaced by Load and Save buttons which will operate directly on your files. Note: Your browser will ask you to grant permission to this "unsigned" applet, and you'll have to agree to this for it to work.


Virtual Clipboard (for large files)

The Virtual Clipboard lets you paste data into or copy data out of multi-page windows. The ---> VC and <--- VC buttons move data to and from the virtual clipboard. If you see a "Browse" button below, then your browser will also let you copy a file on your machine to the Virtual Clipboard. You can then paste it from the V.C. into the calculator's input windows.

Name of file:

Note: if you get a "Save As..." dialog box when viewing the virtual clipboard, it is because the data there is in a binary format (e.g. a PICT file saved from TreeToy). You should specify an appropriate name (e.g. myplot.pict instead of viewclip.php) before saving it.


The Virtual Clipboard is Brainless

Is your window full of garbage after pasting? Unfortunately, the Virtual Clipboard knows nothing about file formats, so cutting and pasting directly from an Excel file will fill your window with junk (ie. raw Excel file bytes). You can, however, copy from the open Excel worksheet to a text editor, then save as text in a new file which you can then copy to the Virtual Clipboard. You can also just save a copy of your Excel file in tab-delimited text format, and copy that file to the VC. The point of the VC is just to help work around the limitations on window size in Netscape, MS Explorer, and probably other browsers.

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Note on Pages

Some browsers limit the size of text windows, so this program allows for bigger input and output using multiple pages. Each page is limited to around 10000 characters. To see if you have filled a page, try typing more characters at the end of the window. When you copy/paste in and out of this program, you have to do so one page at a time; the program has no control over cut/paste, and so can't tell when your input is bigger than one page. Use the Virtual Clipboard above to copy/paste large files.

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This calculator is by John Brzustowski - feel free to send me comments or questions. The source code for this free software is available here