LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence

[LAMARC logo]
LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its sister program Migrate are successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being supported. The programs are memory-intensive but can run effectively on workstations; we support a variety of operating systems.
The LAMARC package is not in any immediate sense derived from the work of Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck (1744-1829). The similarity of names is mostly accidental. But all evolutionary biologists do owe him a debt. Lamarck is an unfairly maligned figure. In addition to being one of the greatest figures of invertebrate biology, he was one of the founders (with Buffon) of the theory of evolution, and the first to propose a mechanism for evolution. You may want to read more about his life and work. [Lamarck himself]
This material is based upon work supported by the National Science Foundation under Grant No. 0814322. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

News and Updates

December 11, 2013 Lamarc 2.1.9, This is an important bug fix release. Bugs fixed are:
  • FIXED: multiple severe bugs in inference of population divergence. All analyses involving population divergence should be re-run.
  • FIXED: failure of DNA or SNP runs with invariant loci. If your run completed successfully you did not encounter this bug and re-running is not necessary.
  • FIXED: lam_conv file converter wrote a multi-population XML file for some single-population cases. If your converted file led to a successful run you did not encounter this bug and re-running is not necessary.
January 7, 2013 WARNING: The inference of population divergence in Lamarc 2.1.8 contains a serious bug. We are working on a fix and will release it as soon as possible. In the meantime, please do not rely on any results involving divergence (other functionality is not affected). We apologize for this error.
May 29, 2012 Lamarc 2.1.8, This is an important bug fix and new feature release. Bugs fixed are:
  • FIXED: major bug for all runs modeling migration. All runs which inferred migration should be re-run. In addition, a bug in the reporting of migration start values has been fixed.
  • FIXED: bug affecting runs sampling a significant number of trees modeling negative growth. Runs modeling growth should be re-run unless they were Bayesian runs with growth priors not allowing negative growth.
New features and improvements are:


January 21st, 2011 Lamarc 2.1.6, This is an important bug fix release. Bugs fixed are:
  • FIXED: major bug with data likelihood calculations for runs modeling recombination. All runs which inferred recombination rate or held it to a non-zero value in versions 2.1.2 through 2.1.5 should be re-run.
  • FIXED: calculation of invariant data term for SNP data modeled with a per-base error rate. All 2.1.5 runs which used the data uncertainty model on SNP data should be re-run.
  • UPDATED: random number generator to use the Boost library, and added guards against returning values of exactly 0 or 1 for double values. No previous runs need be re-done, but if you had a data set with an unexplained crash, this may fix it.


May 10th, 2010 Lamarc 2.1.5, This is a minor bug fix/enhancement release. Improvements include:
  • Improved output reporting
  • Compiles with g++ 4.3.3
  • Minor user experience improvements
  • data uncertainty model (beta test)


March 4, 2009 Two publications relevant to Lamarc:

General

All methods presented here use the coalescence theory of Kingman (1982a, b) and estimate population parameters like effective population size, growth rate, migration rate. To achieve this, the methods sample random genealogies of sequences (or alleles) and calculate the parameters. Since this is an integration over almost an infinitely large tree space, the methods use a Metropolis Monte Carlo sampling technique to concentrate the sampling in regions which contribute to the final result.

LAMARC is written in C++ and is also available as executables for Windows, MacOS and Linux. It will compile on most workstations. You can find more information to the individual programs following the links below:

Programs available:

[Lamarc icon] Lamarc estimates the effective population sizes, population exponential growth rates, migration rates, and per-site recombination rate of n populations using DNA, SNP, microsatellite, or electrophoretic data. It can also perform trait mapping. (Last update: July 2008)
[Migrate icon] Migrate estimates the effective population sizes and migration rates of n constant populations using nonrecombining sequence, microsatellite or enzyme electrophoretic data. Migrate is now maintained by Peter Beerli at Florida State University.

Older programs (for reference):

[Recombine icon] Recombine estimates the effective population size and per-site recombination rate of a single constant-size population using sequence or SNP data. (last updated: June 2002)
[Fluctuate icon] Fluctuate estimates the effective population size and a exponential growth rate of a single growing population using nonrecombining sequence data. (last updated: September 2002)
[Coalesce icon] Coalesce estimates the effective population size of a single constant population using nonrecombining sequences. (last updated: September 1995)


Papers and Posters available:

[Lamarc icon] [PDF Document] Paper introducing LAMARC 2.0 (also available from the Bioinformatics web site).
[Lamarc icon] [PDF Document] Poster presented at the EVO-WIBO meeting 2006 in Port Townsend, Washington .
[Migrate icon] [PDF doc] Paper about Migrate (n-population version).
[Migrate icon] [PDF doc] Paper about Migrate (2-population version).
[Fluctuate Icon] [PDF doc] Paper about Fluctuate.
[Coalesce icon] [PDF doc] Paper about Coalesce.


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Get help:


Mary K. Kuhner & Jon Yamato mkkuhner@uw.edu Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA 98195-5065, USA. Phone: (206) 543-8751, fax: (206) 685-7301

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