Restriction fragment similarities

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Fri Jul 19 12:37:41 EST 1991


Johnjoe McFadden asks if there is a way to take a similarity matrix
generated from +/- data from RFLP patterns and use it as the bases for input
to phylogeny programs.  Of course there are methods that can use the +/-
data directly (parsimony, for example) but I assume that distance matrix
methods were intended.

Nei and Li (PNAS 1979) proposed a distance measure for such cases, which is
basically a variant on -ln(S) where S is the fraction of fragments shared.
It is not hard to write a program to calculate it, and perhaps one could
find a way to do it with a spreadsheet program.

Joyce Miller, who can be reached through the Department of Agronomy,
University of Wisconsin, Madison, Wisconsin 53706 (last I heard) has a
package, RESTSITE, for PCDOS that computes this measure.

It is a limitation on my own package that I don't happen to have put a
program in to compute this measure.  I will in the next release (3.5, due
who knows when.  But it is really not hard to write a program in, say,
BASIC that reads the data files and writes a distance matrix compatible with
existing packages.

-----
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at genetics.washington.edu     (IP No. 128.95.12.41)
 Bitnet/EARN:      felsenst at uwavm
 UUCP:             ... uw-beaver!evolution.genetics!joe

Let's all hope the human-chimp hybrid discussion goes to the
POPULATION-BIOLOGY group and does not come here (it's not molecular anyway)!



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