View Dean's "McGee Network Creation Demonstration" before beginning.

1. Go to your GAP page on FTDNA and generate a yDNA Results table
(alternately, you can use your table on your free FTDNA group webpage
since it will not copy any unnecessary headers)

2. Click on the table. Select all.

3. Go to Dean McGee's yDNA comparison Utility at
http://www.mymcgee.com/tools/yutility.html

4. Follow the directions and click on the options you need

5. Make sure you click on ONLY the markers you are comparing at the
top of the Utility. Also, click on the Fluxus option.

6. If you only want to do a 12 or a 25 marker comparison, delete all
the markers you are not comparing on the sequences and/or delete
everyone who has not upgraded to the specific marker set you are
comparing. Make sure there are no extra spaces at the end of the
lines. You can make sure of this by highlighting the row and see if
there is extra space after the last marker.

7. Click on execute.

8. A separate window will open with the generated comparison tables.

9. In the middle of that window, you will see the Fluxus output to cut
and paste to word or notepad.

10. Save the file as "Your File Name Blah Blah.ych"

11. Open Fluxus. Click on import rdf file (you can change this on the
little file search menu to look for your .ych file instead.

12. Select the file, Select Median Joining, Calculate Network, Save
the file as "Your File Name.out"

13. Finally, use the .out file you produced and Draw Network. Color
and adjust.

IMPORTANT: The yUtility may take a while to generate the tables. You may see
a warning that that says another App is running which may cause your
PC to run slowly. It asks if you wish to abort, DON'T, unless it
really is taking too long. Click "Cancel" to allow it to finish. Keep
clicking cancel if it pops up.

Fluxus Network no longer has an option to save the image of your
network, use an inexpensive Screen Capture application once you have
colored the groups, and changed whatever else I need to. The Screen 
Capture Application allows you to add captions, arrows, etc.

You can get a Quick Screen Capture shareware one at
www.etrusoft.com Purchasing it allows you unlimited upgrades.

To see an example of a Phylogenetic Diagram:

http://www.familytreedna.com/public/Amerind_Y   (Click: "Results")

An easier way that saves time and your finger is to place your cursor
at the END of the row, hold down shift and hit end. The extra space
highlights and you can delete it. Caution, it will bring up the
succeeding row right next to it so don't get trigger happy with the
delete key. Hit enter and move on to the next one. I've learned these
little things by trial and error over the past two years.

Tips:

Save the sequences you pasted in the DATA box once you make
adjustments and have hit execute to produce your comparison tables and
see that they are correct. You can then manually add any new members
as you get results and not have to do the whole process again. They
only come a few at a time so it won't be difficult. Do the same for
your 12 marker group, your 25 and 37.[1]

Bennett Greenspan advised me to base the tree chart on the 25 marker results
because the 37 would be too "three-dimensional." The 25 worked well at first,
but when my project got to a certain size I found that I had reached that overly
three-dimensional point, the lines between nodes were no longer were
proportional to the genetic distance, and the positioning of the nodes were no
longer accurate.[4]  Example: Burns Phylogenetic Charts

Marker conversion: Example:  FTDNA data for D389-2 should be 29, not 16 in
the FTDNA format.  But for the phylogenetic tree D389-1 should be
subtracted so any mutation on that marker isn't counted twice.  The
yutility will display the value of 29 in the haplotype table but put
16 in the .ych data.[3]

Another trick when using Fluxus, is that you don't need to delete markers you
don't want to appear on your diagrams, such as 464. Just set their weightings to 0.
That way you can easily go back and change them if you wish.[6]

PRINTING

ALWAYS SAVE THE ORIGINAL!  Recommended file extension - .bmp
Saving as .bmp will allow mistakes to be corrected before saving as .jpg

.fdi Format

Save as a .fdi extension gives the ability to:

1. Change the colors
2. Add patterns and slices to large globes
3. Adjust the links
4. Remove the nodes
5. See only the DYS mutations
6. Left click to see who was in a particular globe if the haplotype
was shared and you are missing someone
7. Zoom in or zoom out
8. Save or capture that image again as a different file

IrfanView
http://www.irfanview.com

When your network diagram is showing and sized the way you want, press
ALT-PrtScn on your keyboard.  This will copy the image to your
clipboard.  Then open IrfanView and select Edit-Paste.  Then drag your
mouse around the area that you want to make into an image and select
Edit-Crop Selection. IrfanView will shrink to only display the selected
area.

Then select File-Save or Save As.  You can save in many file types.  I
prefer GIF images for these -- the characters won't get mangled like
they do many times with .jpg.  With .gif format, you can select a
transparent color if you want the background of the image to blend into
the background of your web page.[2]

From Ana's ISOGG Enhanced Phylo-Tree Workshop - 4 Nov 2006[5]

Quick Screen Capture
http://www.etrusoft.com/download.htm (well worth the $20)

Work in Bitmap and then save the product by converting to .jpg, .tff or a similar format

Instructions:

1.      1.   Start at FTDNA’s GAP page

2.   2.   Pick the group and the markers you want to plot

3.   3.  Copy and Paste what you want into Dean McGee’s Utility

4.   4.  Use the curser and “end” key to take out all the spaces that are not needed

5.   5.  “Execute”