06
Jul
2010
portaluser

LAMARC

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence; Kuhner 2006) is a package of programs for computing population parameters, such as population size, a recombination rate, population exponential growth rate and migration rates by using likelihoods for samples of data (DNA or RNA sequences, SNPs, or microsatellites) from populations. It approximates the summation of likelihood over all possible gene genealogies that could explain the observed sample. The programs are memory-intensive but can run effectively on workstations or modern microcomputers. The package is continually expanding and more executables for different machines will become available soon. LAMARC currently has four core functions: estimation of the effective population size, estimation of
the exponential growth rate of a single growing population, estimation of migration rates, and estimation of per-site recombination rate of n populations. These estimates are calculated using microsatellite data or enzyme electrophoretic data (Beerli 2006).

Documentation: 

Online documentation is available from the LAMARC web site.

Meaning of the g parameter in LAMARC

Pluzhnikov & Donnelly (1996) describe the relationship between sample size and genetic variation when making experimental design decisions.

Input Format: 

LAMARC requires infiles to be in XML format; however, the Lam_Conv utility will convert PHYLIP files into XML.

Example data files:

* Example DNA sequence data set (view, download)
* Example enzyme electrophoresis data set (view, download)
* Example microsatellite data set (view, download)

Instructions for All: 

Instructions

To convert PHYLIP files into XML use the converter. In the terminal window type:

lam_conv

To run LAMARC locally, type the program name at a terminal window prompt:

lamarc