You must set up your file with the haplotypes as a .csv file (comma separated variables). You can create this with a text editor, but it is probably easier to use a spreadsheet program and export it as a csv file.
In a spreadsheet program such as Excel, use column A for the haplotype identification. The identifier can be any text, but the program will only read and use the first 20 characters. The haplotype should start in column B with marker DYS393 and use the FTDNA order thereafter. For a 37-marker haplotype, the last marker, DYS438, should fall in column AL If some haplotypes have more than one value for DYS019 or DYS464, these should be omitted.
DYS389ii should be represented as the sum of the two parts of this marker.
You can use more than 37 markers if you like, but some of the minor haplogroups, such as Haplogroup H, do not have sufficient data for some of the markers, and these haplogroups will drop out of the analysis if these markers are used. If you use markers beyond the FTDNA 37, use the same order that is displayed on the data entry page of the web-based program (FTDNA version). After the last marker you want to include is entered, you don't need to add anything to terminate the list of marker values. To export the data to a csv file, click File, then click Save As, then at the bottom of the save menu in the Save As Type window, change the file type to CSV (you may have to scroll down the list of available types to find it). Set the file name and then Save. In Excel, you may be asked "Are You Sure You Want to Do This?", but just answer Yes and continue to save.
You should have the first haplotype in the first row of the file. Do not include any column headings (you can use column headings to aid in creating the file, but remove them before saving).
If you create the file directly as a csv file in a text editor, the identifier and each marker value should be separated by commas. If a marker value is missing from the FTDNA set, just type a second comma and continue. Following the last marker value, you do not need trailing commas.
If you have a value reported as "missing" by the testing company, you should put "89" in the cell for that marker. If you put anything else in the cell (other than a numeric value), the marker will be ignored in the analysis.