L. David Roper (firstname.lastname@example.org)
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:
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