Brief Instructions for Using the PHYLIP/Neighbor or Kitsch Programs to Calculate and the TreeView Program to Plot Phylograms

L. David Roper (

The PHYLIP and TreeView programs can be downloaded at:

The following rules describe how I use the Neighbor or the Kitsch program of PHYLIP to calculate a phylogram tree file for the 25 Y-chromosome markers:

For another description of the procedure given above see CalculateAndPlotPhylograph.pdf .

Here is an example input file for 25 Y-chromosome markers: Roper.txt

Here is the phylogram created by the rules above for the Roper.txt file:

Note the scale in the lower left corner: The distance shown is 0.1 relative mutations. For long times for 25 markers, 1 relative mutation is about 500 years, assuming a generation is 25 years and the average mutation rate is 1/500. The extreme right is the present time. Do not use this calculation for short times, because a mutation can occur in 1 generation or 25 years. You can use the scale to label the the earliest-time junctions with the time before the present (ybp). I use the MS Paint program to do this. The PHYLIP Neighbor UPGMA/TreeView calculation/plot does not give a good representation of the data for Y-chromosome marker sets when several of the testees only differ by one relative mutation. However, it does rather faithfully show the large relative mutations.

On my 3.06 GHz machine it took slightly over one hour to do a PHYLIP/Kitsch calculation for the relative mutations of 128 individuals with 10 jumbles.