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:

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

393,390,19,391,385a,385b,426,388,439,389a,392,389b
(blank line)
(blank line)
SCL
13,23,15,10,14,15,11,14,11,12,11,17
1
LLL
13,25,14,12,11,14,12,12,12,13,13,16
DCL
13,25,14,11,11,14,12,12,12,13,13,16
1
TML
13,24,15,10,12,15,12,13,12,13,12,16
1
JMAL
13,24,15,10,12,15,12,13,12,13,13,17
1

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