2. Create a new directory on your computer to hold the haplotype file from step 1, and the other two files that will be mentioned below.
3a. For the basic 21-haplogroup analysis, download the file hapest5data.js at the following link: here. If you use IE7, just click on the link and IE7 will ask you where you want to save it (save in the directory created in Step 2). If you use Firefox, RIGHT click on the link and choose "Save Link As" to download the hapest5data.js file. Specify the directory you created in step 2 as the destination directory. If your browser is set to download all files to your desktop, then the file will end up there and you'll have to manually copy it to your directory.
3b. For the largest number of haplogroups in the analysis (currently 27), follow step 3a EXCEPT download the file hapest5data.js from the following location: here
4. Following the same procedure as in Step 3, download the file hapestjsbatch.exe at the following link: here and save it in the same directory. Note that there is only one version of this program and that it works with either version of the file hapest5data.js.
5. Run the program hapestjsbatch.exe (you can just browse to the directory on your computer where you saved it and double-click on the file name). The program will ask you the name of your input haplotype file (include the .csv extension), and then it will ask you the name that should be given to the output file the program creates. For example, the input file might be named Mydata.csv, and the output file might be named something like Mydataout.txt The output file will be a text file with fixed column widths and positions (and can be imported into Excel). The program will also ask you for three other pieces of information--the region of Europe the haplotypes come from, the minimum haplogroup score and minimum probability you want to use to get a haplogroup name in the prediction column (Suggestion--start with a minimum score of 40 and minimum probability of 95 [%]). If the score or probability from a haplotype fails to meet your criteria, the prediction cell will be left blank for that haplotype. However, all of the scores and probabilities will still be returned by the program in the output file. The program will only take a few seconds to complete a couple of hundred haplotypes. After the output file is created, you can import it into Excel or another spreadsheet program (In Excel, choose "Import External Data from the Data menu, then select the "Fixed Width" option), or just print the output file as it stands from a text editor program.