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provided by the Ewing Family Association.
Creating Network Diagrams
I use Fluxus
Engineering's free shareware program, Network, infrequently enough that I have
to spend a little time each time I do it figuring out how it works all over
again. Today, I made myself a set of directions for displaying Y-DNA STR data in
median joining network diagrams, and I thought maybe some of you would find
these useful--especially if you haven't used this program before. You can get
the program from
*FLASH*: A user guide is available at http://www.fluxus-engineering.com/Network4510_user_guide.pdf.
If you are going to make this work, you need to pay careful attention to file extensions--when you try to open the files you make, the default file type is almost always wrong, which makes it so that you can't find your file unless you change the file type in the "Open" window. Anyhow, maybe these instructions will help you get started with a useful but not very intuitive program. If not, they didn't cost you much.
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1. Prepare an Excel file with participant IDs in the first column and markers in FtDNA order (or use another standard order, but be sure to tell the McGee program what order to use in step 3 below).
2. Copy the IDs and all the markers, but if you have the marker names in the first row, do not copy those.
3. Go to http://www.mymcgee.com/tools/yutility.html?mode=ftdna_mode.
4. Under "Generate Tables" check the box "Generate Fluxus phylogenetic network.ych data" and uncheck all the other boxes except "FTDNA order haplotype comparison."
5. Under "General Setup" uncheck "Show Status." Depending on whether you want a modal haplotype calculated from your data to appear in your completed network diagram, you can check modal haplotype or not, as you wish. The Network program will treat the modal as if it were another individual.
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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, labeled "Fluxus data..." select everything in that window (click in the window somewhere and press Cntrl+A), and then copy and paste it into a text file. I use my Notepad utility for this.
8. With your text file open, click "Save As." Under "Save as type" choose "All files." Name the file what you wish, followed by .ych. it is crucially important that the file extension be .ych. Save it on your desktop.
9. 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.
10. Open the Network program. (This is available as a free download from http://www.fluxus-engineering.com/.)
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11. Click on "Calculate Network" then "Network Calculations" then "Median Joining".
12. in the new window, click on "File," then "Open," and then in the "File Type" pull-down menu, choose "Y-chromosomal data file (*.ych).
13. Navigate to the .ych file you made with your plain text program and click open.
14. It won't look as though anything has happened, but click on "Calculate network" again and you will see some action.
15. A "Save As" window will appear with a default file name the same as your .ych file except with a .out extension. This is a good name to use. Just click "Save."
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16. You will get a message, "File saved successfully. You may proceed to the Draw Network menu to draw your *.out file." Click OK.
17. A new window will open. Click on "Draw network." Another window will open.
18. Click on "File," then "Open," and then 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.
19. You will get message "The torso has been completed. Do you wish to modify the torso?" Click NO.
20. A diagram will appear. At this point, you can do a tremendous amount of fooling around. If you 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. As a rule, you don't want to do this, because the line length is proportional to the genetic distance. If you do something you don't like, click "Undo." I move things around so they are not stacked on top of one another too badly. If you can't get a hold of something, zoom in so that you can see what you are doing better.
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21. When you are done with this preliminary fooling around, click "Finalize" and you can fool around some more.
22. Now a diagram with node names, "median vectors," and mutated positions appears. Uncheck "Display mutated position" or you won't be able to see anything.
23. I usually find that changing font size to 10 works best for me. Then right click on a node name (not the node, the name), change font style to "Bold," check "Apply to all taxa" then OK.
24. 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."
25. 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 diagram, each node is labeled only with the ID of the first individual of that haplotype.
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26. Right click on a node and you can change the color of the node or add pie slices and color them how you like.
27. When you are done fooling around, uncheck "Show median vectors." For my purposes these just clutter up the diagram, but you can't move the nodes around while preserving the line lengths without having these show, so get rid of them last.
28. If you don't have too many individuals, or if you aren't using too many markers, you might want to click "Display mutated positions" again. This will put the mutations along each link. You can change the color, size and style of type by right clicking on one of the mutation names.
29. When you are all done, you can print the result from the File menu, but the result is pretty rough to my taste. I have had better luck by making a screen shot jpeg by pushing Alt+PrtScn, and then pasting it into another document (I use PowerPoint, but I suppose lots of different programs would work for this) for cropping and resizing by pushing Ctrl+V.
30. When you close, Network will ask if you want to save the diagram. It will save your diagram as a .fdi file, but opening it is a little tricky. The first time you open it, your machine won't know which program to use. Tell it to always use Network to open this type of file. Then Network will open to its start screen. Click on "Draw network," then "File," then "Open," then change the "Files of Type" pull-down menu to "Formatted diagrams (*.fdi)" and then you can open your .fdi file.
Whew! No wonder it took so long to figure out how to do this. Good luck.
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