Migrate-n

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Description

migraten website  

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.

Required Modules

modules documentation

Serial and Threaded

  • migraten

migrate-n and migrate-n-threaded binaries will be made available.

The minimal command is "migrate-n parmfile -nomenu"

Parallel (MPI)

Required modules:

  • intel/2016.0.109
  • openmpi/1.10.2
  • migraten

Binary:

  • migrate-n-mpi

Run it with "mpiexec migrate-n-mpi parmfile -nomenu"

System Variables

  • HPC_MIGRATEN_DIR - installation directory
  • HPC_MIGRATEN_BIN - executable directory

Additional Information

A manual page is available. Run man migrate to view it after loading the appropriate module.

Full manual is available from the Migrate-n website.


Job Script Examples

See the Migrate-n_Job_Scripts page for migraten Job script examples.