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[Q] any software to compute Nei and Li coefficient?

Ken Rice rice at green.harvard.edu
Wed Mar 29 13:16:19 EST 1995


In article <3lbev2$qf2 at mserv1.dl.ac.uk>,
JAMES O. MCINERNEY <James.Mcinerney at UCG.IE> wrote:

>Hi,
>
>Does anyone know of any software that calculates Nei and Li's coefficient
>for studying genetic variation in terms of restricition endonucleases:
>
>PNAS 76, 10, 5269-5273 (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases.

I don't have Nei and Li's paper at hand, but ...

My program RSVP (restriction site variability program) calculates several 
measures of genetic variability based on restriction map data.  These
include nucleotide diversity measures by Nei and Tajima, and nucleotide
polymorphism and theta=4Nu estimators by Ewens, Engels, Hudson, and by me.  

It also produces Jukes-Cantor corrected distance matrices with standard 
errors from collections of restriction maps, and it gives measures
of interpopulation variability between two sampled populations.

C source code for Version 2.08 of RSVP is available for anonymous 
ftp from: 

         ftp://oeb.harvard.edu/rice/rsvp.2.08.tar.Z

or you can get it on WWW from:

                http://oeb.harvard.edu/~rice

RSVP runs under Unix, but other users have reportedly compiled
it under MSDOS.  It is reasonably easy to use -- command-driven with 
extensive online help.

Ken Rice






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