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Recombine 1.40 in LAMARC package now available

Mary K.Kuhner mkkuhner at kingman.genetics.washington.edu
Tue Oct 31 12:28:39 EST 2000


We have just released Version 1.4 of RECOMBINE in the LAMARC package.

RECOMBINE makes a maximum-likelihood estimate of per-site recombination 
rate and Theta (4Ne*mu where Ne is the effeective population size and 
mu is the per-site mutation rate) using samples of DNA, RNA, or SNP data 
from a single population.

The algorithm is Metropolis-Hastings Markov Chain Monte Carlo sampling.
We create a large cloud of possible recombinant genealogies for the
sampled sequences, and infer the parameters from the entire cloud.
This should be more powerful than pairwise estimators, and does not
require that we can infer the recombinant genealogy accurately.

A paper describing this algorithm will be in the November issue of
GENETICS:  MK Kuhner, J Yamato and J Felsenstein (2000), Maximum 
likelihood estimation of recombination rates from population data.

Version 1.4 adds three major capabilities:

--Analysis of SNP (single nucleotide polymorphism) data using 
the algorithm from Kuhner, Beerli, Yamato and Felsenstein, Genetics 2000.  
--Estimation from phase-unknown (unhaplotyped) data using the 
algorithm from Kuhner and Felsenstein, Genetic Epidemiology 2000. 
--A "heated chain" search technique to improve the efficiency of
its search, following an algorithm suggested by Geyer (this is
particularly useful for phase-unknown data).

Several bugs have also been fixed.  In particular, the likelihood
table was sometimes garbled, certain Alpha machines had crashes due to
numeric underflow, and (despite the program's claim to analyze
SNPs) SNP analysis did not work.  We believe that results from 
previous use were not materially affected by these bugs; it's not
necessary to rerun previous work, unless the program crashed
or garbling was visible.

The program is freely available (as source code, Mac executables, or
Windows executables) via WWW:

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

and via anonymous ftp:

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

We would like very much to hear about any publications that result from
use of the LAMARC programs, as well as any bugs, questions, or suggestions
for improvement.

Mary Kuhner
mkkuhner at genetics.washington.edu

Department of Genetics, University of Washington
Box 357360
Seattle, WA 98195-7360

(206) 543-8751


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