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.

Availability

Program is available in version 3.1.6, 3.2.20 and 3.6.10.

Use

Inicialize environment by command

module add migrate 3.6.10

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

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


For older versions: Initialize environment for one processor "module add migrate-3.1.6" or "module add migrate-3.2.20", for multi-processor MPI version "module add mpich-p4 migrate-3.1.6-mpi" or "module add openmpi migrate-3.2.20-mpi" for SHM version "module add migrate-3.1.6-thread" or "module add migrate-3.2.20-thread" and run "migrate-n".

Documentation

Documentation is available on WWW server.

Program administrator

meta@cesnet.cz

Homepage

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