🚀 go-pugleaf

I have a client who has presence / absence data for DNA fragments
from 5 individuals for each of 10 different geographic
populations of a species of insect. The DNA fragments show as
bands on a gel. There are a variable number of bands per
population. The data looks like this:

                               Band
Population  Individual   1 2 3 4 5 6 7 8 9 ...
         1           1   0 1 1 0 1 0 0 0 0
                     2   1 1 0 1 1 0 0 0 0
                     3   1 1 0 0 1 0 0 0 0
                     4   1 1 1 1 1 0 0 0 0
                     5   0 0 1 0 1 0 0 0 0

         2           1   0 0 1 0 1 1 1 0 1
                     2   0 0 1 1 0 1 1 1 0
                     3   0 0 1 0 0 1 0 0 0
                     4   0 0 1 1 0 1 1 0 1
                     5   0 0 1 1 0 1 1 1 1
etc.
Let x    = 1 if the band k is present in population j, individual
     ijk     i, and 0 otherwise.

She wants to calculate a similarity matrix betweem populations
which reflects the number of shared bands between individuals.
She has a paper by Nei and Li, "Mathematical model for studying
genetic variation in terms of restriction endonucleases." Proc
National Acad Sciences USA (1979) which defines a general
similarity coefficient between populations in a theoretical
manner without giving any computational formulae.

Could someone who has used this approach, or any other define the
computational formulae in terms of my data, x    , above?
                                             ijk

Thanks for your help.

David Baird    Biometrician

Mail address:  AgResearch, PO Box 60, Lincoln, New Zealand
Internet:      BairdD@LAN.Lincoln.CRI.NZ
Phone:         +64 3 325 3011
Fax:           +64 3 325 2946