Brief Instructions for Using the Phylogenetic Network Program

L. David Roper (roperld@vt.edu)
(www.roperld.com)

The official brief instructions for using the program are at http://www.fluxus-engineering.com/netwinfaq.htm.

The phylogenetic network program projects an x-marker dimensional space onto a 2-dimensional or 3-dimensional space (drawn in 2 dimensions), so there are many ways to do it. The program does it in three different ways.

Here are some rules I have learned:

• Try a reduced-median calculation first. If it is not too complicated looking, use it. (I always put RM on the end of the file name for this calculation.)
• If the reduced-median plot is too messy, then do a median-joined calculation. If it is not too complicated looking, use it. (I always put MJ on the end of the file name for this calulation.) Some information about genetic connections is lost compared to a reduced-median calculation.
• If the median-joined plot is too messy, then do a median-joined calculation starting from the reduced-median file (*.rmf) file created in the first item above. (I always put RMMJ on the end of the file name for this calculation.) Some information about genetic connections is lost compared to a median-joined calculation.
• Finally, plotting the network (Draw Network menu item in the Network program) is somewhat complicated. After the drawing is completed, there are some choices for zooming in out or and panning (called navigating) at the bottom. When done with those items, click on Finalize at the bottom right corner to show a menu on the right hand side for selecting various items to display.
• Then you can print the plot by doing File-Print. You can save the file by doing File-Save As; then choose file type to be *.bmp and get rid of the .dia on the end of the file name. You will get a huge bmp file (~6 Mbytes). Put it in some graphics program and convert it to a very small jpg file. You can also use a graphics program to annotate it.

Here is an example input file for 12 Y-chromosome markers:

The first line contains the names of the Y markers (with DYS prefix understood); only 6 characters are allowed for each marker name. The next two lines must be blank. The DYS389-1 and DYS389-2 markers must be converted to DYS389a=(DYS389-1) and DYS389b=(DYS389-2)-(DYS389-1, as they are the true alleles. The symbols for the participants (e.g. SCL) must not be longer than 6 characters. The line after the marker values is the frequency; i.e., how many participants have that marker set. (E.g., I use MUR as the symbol for the Majority USA Roper family and several participants have the same marker values.)

For 25 markers the first line should be: 393,390,19,391,385a,385b,426,388,439,389a,392,389b,458,459a,459b455,454,447,437,448,449,464a,464b,464c,464d