LAMARC: RECOMBINE program available

Mary K. Kuhner mkkuhner at evolution.genetics.washington.edu
Wed Jun 17 18:15:58 EST 1998


We would like to announce availability of a new program,
RECOMBINE, in our LAMARC package of programs to estimate
population parameters based on molecular data.

RECOMBINE estimates the per-site recombination rate
(assumed to be constant across the sequence) using
Metropolis-Hastings Monte Carlo sampling of possible
genealoties.  The program works on DNA or RNA sequences, 
or sets of Single Nucleotide Polymorphisms, and makes 
a maximum likelihood estimate of two parameters.  One 
parameter is Theta, defined as 4 x population size x neutral
mutation rate; the other is r, defined as recombination
rate per site over mutation rate per site.  Output
includes a maximum likelihood estimate of each parameter,
and a plot showing the likelihood curve in both parameters.

A general description of the method can be found in
our papers (Kuhner et al. 1995, Genetics 140: 1421-1430;
Kuhner et al. 1998, Genetics 149: 429-434).  A specific
description of RECOMBINE is in preparation.

The program and documentation can be obtained via the WWW at:

http://evolution.genetics.washington.edu/lamarc.html

Or it can be fetched via anonymous FTP at:

evolution.genetics.washington.edu, directory /pub/lamarc/recombine

C source code, PowerMac executables and Windows95 executables
are available.  The program is free.  If it is used to analyze
data for publication we would very much appreciate hearing about
the results.

Mary Kuhner mkkuhner at genetics.washington.edu
Department of Genetics, University of Washington
Box 357360
Seattle, WA 98195-7360, USA

(206) 543-8751




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