LAMARC: Migrate update and extension to n population

Peter Beerli beerli at evolution.genetics.washington.edu
Thu May 28 10:12:04 EST 1998


I have upgraded and extended Migrate (first released on May 1st 1997)
which is part of LAMARC -  Likelihood Analysis with Metropolis Algorithm using Random Coalescence.
LAMARC's web page is http://evolution.genetics.washington.edu/lamarc.html.

Migrate estimates effective population sizes and migration rates between two or 
n populations assuming a migration matrix model allowing for asymmetric 
migration rates and different subpopulation sizes. Migrate is
a maximum likelihood estimator with a Metropolis-Hastings importance
sampling scheme using coalescent genealogies with migration events.

Now available are:
Migrate-0.4 - two-population version
Migrate-n   - n-population version

Both programs allow:
- DNA sequence data: F84 model allowing for unequal base frequencies,
  and substitution rate variation, and weighting
  schemes(similar to DNAML ofof the forthcoming PHYLIP version 3.6)
- Microsatellite data: exact stepwise mutation model, Brownian motion
  approximation to the stepwise mutation model.
- electrophoretic allele data: infinite allele model
- For sequence data a variety of possible rate variation and weighting
  schemes can be used (similar to DNAML of PHYLIP version 3.6)
- Either constant mutation rate or a Gamma distributed
  mutation rate across loci.

Migrate-0.4 delivers:
- Joint estimates of migration rates, and population sizes
- Likelihood surface plots

Migrate-n delivers
- Estimates of all migration rates and all population sizes
- Likelihood surface plots
- Profile likelihood tables
- Approximate percentiles of the parameters using the profile likelihoods
- Likelihood-ratio tests

You can fetch the C-source code or the executables
(Macintosh, Windows95, LINUX, DUNIX, SUNOS, NEXTSTEP) and read more at

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

We request that you register, so that we can send you information about upgrades 
and we know how many scientists are using our programs.

If you have question concerning Migrate, feel free to ask
Peter Beerli (beerli at genetics.washington.edu)

Also available at the same site are
Coalesce - estimates the population size of a single population
           using sequence data
Fluctuate - estimates the population size and exponential growth rate
           of a single population using sequence data.
[Questions concerning Fluctuate and Coalesce should be addressed to
Mary K. Kuhner (mkkuhner at genetics.washington.edu)]


Peter Beerli
-----
Peter Beerli <beerli at genetics.washington.edu>
University of Washington, GENETICS, Box 357360,
Seattle WA 98195-7360  USA.
Work:(206) 543-8751, Fax:(206) 543-0754; GMT+0800.
http://evolution.genetics.washington.edu/PBhtmls/beerli.html




-- 
-----------------------------------------------------------
Peter Beerli <beerli at genetics.washington.edu> 
University of Washington, GENETICS, Box 357360, Seattle, 
WA  98195-7360,  USA. Work:(206) 543-8751,




More information about the Mol-evol mailing list