Release 1.2.1 of LAMARC

Mary K.Kuhner mkkuhner at kingman.gs.washington.edu
Tue Jun 8 16:12:16 EST 2004


We have just released version 1.2.1 of the LAMARC program (part of the
LAMARC package).

LAMARC uses genetic data from a population to estimate several population
parameters:  size of subpopulations, subpopulation growth rates, migration
rates among subpopulations, and overall recombination rate.  The algorithm
is Metropolis-Hastings MCMC; we search through a wide space of genealogies
representing the possible histories of the data.

Suitable data for this program includes DNA or RNA sequences, SNPs, or
microsatellites.  Phase may be known or (with some loss of power)
unknown.

We had a brief and unsatisfactory release of version 1.2 several months
ago, which is why this release is 1.2.1.  If you are one of the few
people who obtained copies of 1.2, please replace them.

Version 1.2.1 adds:

Population growth and shrinkage.  LAMARC can now estimate population
growth or shrinkage using an exponential model.  In cases with population
subdivision, a separate growth rate is estimated for each subpopulation.

GTR model for DNA, RNA and SNP data.  LAMARC can now use the General
Time-Reversible model of nucleotide sequence evolution.  The best way
to use this feature is to estimate the GTR rates with a program such
as PAUP* and import them into LAMARC.

Performance improvements.  Maximization of the likelihood surface is
now faster and much more reliable, and the program is faster overall.
It has also been updated to recent C++ standards and will compile
correctly on a wider variety of systems.

LAMARC is written in C++.  We distribute source as well as executables for
Linux, Windows and MacOS.  To obtain the program or simply learn more
about it, visit our web site:

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

or our anonymous ftp site:

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

The LAMARC development team:  lamarc at gs.washington.edu
Mary Kuhner
Peter Beerli
Jon Yamato
Eric Rynes
Lucian Smith
Elizabeth Walkup

Kuhner/Felsenstein Lab
Department of Genome Sciences
University of Washington
Box 357730
Seattle, WA 98195-7730
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