---------- Forwarded message ---------- Date: Fri, 4 Jun 2004 13:57:06 -0700 From: The Lamarc Development Team lamarc@gs.washington.edu To: lamarc-announce@gs.washington.edu Subject: [Lamarc-announce] Lamarc version 1.2.1
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
You are receiving this message because you registered a copy of LAMARC and specifically asked to receive update messages. If you no longer want them, send a message to lamarc-announce-request@gs.washington.edu with the subject 'unsubscribe', or visit the lamarc-announce web page at http://evolution.gs.washington.edu/mailman/listinfo/lamarc-announce or let us know directly by emailing lamarc@gs.washington.edu and we will remove you from the list.
The LAMARC development team: lamarc@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 ____________________________________ Lamarc-announce mailing list Lamarc-announce@evolution.gs.washington.edu http://evolution.gs.washington.edu/mailman/listinfo/lamarc-announce http://evolution.gs.washington.edu/lamarc.html