Fluxus Engineering's free Phylogenetic Network Software website does have, in addition to the free Network Software, release notes and a user guide that you can download. I found the user guide a little difficult to follow but others may not. In Section 2.5 STR data (short tandem repeat, microsatellite data) of the user guide it instructs you how small data sets can be entered manually and saved into a file using Network's Data Editor. However, I find it easier to use McGee’s Y-Utility.

Open McGee’s Y-Utility and scroll down through his Instructions to the dot point “Fluxus Phylogenetic Analysis Software” where he has a 2MB Flash movie of how to create a cladogram/phylogenetic network using Fluxus Engineering’s software. Using it and the instruction below, you should have no problems in creating you cladogram.

  1. Prepare an Excel file with the participant IDs (I used the kit numbers) in the first column, followed by the values of each marker. For this example I used 25 markers results for 17 members.

    25markertable

  2. Go to McGee’s Y-Utility: Y-DNA Comparison Utility, FTDNA Mode. Make sure the heading has FTDNA Mode. McGee also has a utility that uses data imported from Ysearch and the order of the markers is different from FTDNA.
  3. Under "Generate Tables" ensure that “FTDNA order haplotype comparison” is checked, then check the box "Generate Fluxus phylogenetic network.ych data" and uncheck all the other boxes.
    generatetablemcgee

  4. Under "General Setup" if you want a modal haplotype calculated from your data to appear in your completed network diagram, you can check modal haplotype, otherwise leave it blank. The Network program will treat the modal as if it were another individual.
  5. Copy the IDs and all the markers from your Excel file (information in yellow above).
  6. Paste your Excel data into the "Paste haplotype rows here" field and click "Execute."
  7. A new window will open. Scroll to the bottom of the new window to a field labeled "Fluxus data – paste into a .ych file" then right click in the window and “select all” to highlight everything in that window, then right click again and copy everything (you can also press Cntrl+A and then Cntrl+C).

    fluxusdata

  8. Go to your accessories and open WordPad utility and paste the data you copied into a text file.
  9. With your text file open, click "Save As." Under "Save as type" choose "Text Document." Name the file what you wish, I named mine example25markers followed by .ych. It is crucially important that the file extension be .ych. Save it in your documents folder or on the desktop.

    saveychdoc.

  10. Alternatively, if you have this data in a file ending with .txt, you can just change the .txt to .ych but it HAS to be .ych.
  11. Open the Network program.
  12. Click on "Calculate Network" then "Network Calculations" then "Median Joining".

    calculatenetwork

  13. In the new window, click on "File," then "Open," and in the "File Type" pull-down menu, choose "Y-chromosomal data file (*.ych).

    select-ych-file

  14. Navigate to the .ych file you made with your plain text program, select it and click open.
  15. It won't look as though anything has happened, but click on "Calculate network" again and you will see some action.
  16. A "Save As" window will appear with a default file name the same as your (*.ych) file and in the “Save as Type” window you will find "Network output files (*.out)." Just click "Save."

    savenetworkoutput

  17. You will get a message, "File saved successfully. You may proceed to the Draw Network menu to draw your (*.out) file." Click OK.
  18. A new window will open. Click on "Draw network." Another window will open.
  19. Click on "File," then "Open," and change the "Files of type" pull-down menu to "MJ or RM out files (*.out)." Now select the (*.out) file you made in step 15 above and click "Open." You will get message "Diagram is not adapted to the screen. It will be redrawn." Click OK.
  20. You will get message "The torso has been completed. Do you wish to modify the torso?" Click NO if you do not want to modify it. If you do want to reshape it click YES and adjust it using the instructions below. Once you have fine-tuned it to the way you like, click “Continue.”
  21. The cladogram will appear. Below is what the example looked like.

    cladogram25example

  22. To modify your cladogram click on a line, it will become highlighted and you can click and drag either end of it without changing the length of the line. If you click on a node without first selecting a line, you can move the node but this will change the length of the line. You usually do not want to do this, because the line length is proportional to the genetic distance. If you do something you don't like, click "Undo."
  23. When you are done with your experimenting or ready to see the completed cladogram, click “Finalize.”
  24. Now the cladogram will appear with all its data. You can again experiment with the display parameters to get it the way that you like or move the nodes around to be able to see names and median vectors better. You may need to have the vectors on an angle to see the names best.
  25. For this example I changed font size to 12. Then right click on a node name (not the node, the name), change font style to "Bold," check "Apply to all taxa" then OK.
  26. Right click on a line, then change the link color to light gray and check both "Apply to all links outside torso" and "Apply to all links within torso."
  27. Double click on a node and it will show you how many individuals are in the node (these will be individuals with identical haplotypes) and will tell you their IDs. In the cladogram, each node is labeled only with the ID of the first individual of that haplotype.
  28. Right click on a node and you can change the color of the node or add pie slices and color them how you like.

    cladogram25example1

  29. Network User Guide points out that activating the “Display mutated positions” checkbox in Network Draw, will display the mutated position names (red letters and numbers in example above) along the network links. Two characters are appended to the locus name (e.g. “D19aa”) to distinguish between repeat-numbers (e.g. “aa”=10 repeats, “ab”=13 repeats, depending on data file).
  30. If you have a large number of individuals, you may need to unclick "Display mutated positions" so that your cladogram is not to congested.
  31. When you finish, you can save the results as a Bitmap (*.bmp) or in the portable document format (*.pdf). A third way is to make a screen shot jpeg by pushing Alt+PrtScn, and then pasting it into another document such as one in PowerPoint, for cropping and resizing by pushing Ctrl+V.

    saveexample

  32. When you close, Network will ask if you want to save the cladogram. It will save your cladogram as formatted network diagram (*.fdi) file, but opening it later is a little tricky. You need to open your Network program, click on “Draw Network” which will open another window. Click on “File” and then “Open” to bring up the Open Window.

    openfdifile
    In the pull down window “Files of type” select “Formatted diagrams (*.fdi)” then select your file and click on “Open.” You should now be able to see your file that you had saved previous.