Migrate

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Description

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters. It can use the following data types:

  • Sequence data using Felsenstein's 84 model with or without site rate variation,
  • Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)
  • Microsatellite data using a stepwise mutation model or a brownian motion mutation model (using the repeatlength input format or the fragment-length input format),
  • Electrophoretic data using an 'infinite' allele model.

The output can contain: Estimates of all migration rates and all population sizes, assuming constant mutation rates among loci or a gamma distributed mutation rate among loci. Profile likelihood tables, Percentiles, Likelihood-ratio tests, and simple plots of the log-likelihood surfaces for all populations and all loci.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of migrate and load default version of migrate as

module avail migrate/ # list available modules
module load migrate   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail migrate

and choose explicit version you want to use.

then you can run single core, thread or MPI version of migrate by commands

migrate-n-single
migrate-n
mpirun migrate-n-mpi


mpirun needs to set the complete path to the programme ($PATH is not enough)

mpirun $(which migrate-n-mpi) -nomenu
or
mpirun /software/migrate-4.4.3/migrate-4.4.3/src/bin/migrate-n-mpi -nomenu

Documentation

Documentation is available on WWW server.

Homepage

URL: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html